WorldWideScience

Sample records for database search fda

  1. Drugs@FDA: FDA Approved Drug Products

    Science.gov (United States)

    ... Cosmetics Tobacco Products Home Drug Databases Drugs@FDA Drugs@FDA: FDA Approved Drug Products Share Tweet Linkedin Pin it More sharing ... Download Drugs@FDA Express for free Search by Drug Name, Active Ingredient, or Application Number Enter at ...

  2. Drugs@FDA Database

    Data.gov (United States)

    U.S. Department of Health & Human Services — Information about FDA-approved brand name and generic prescription and over-the-counter human drugs and biological therapeutic products. Drugs@FDA includes most of...

  3. FDA toxicity databases and real-time data entry

    International Nuclear Information System (INIS)

    Arvidson, Kirk B.

    2008-01-01

    Structure-searchable electronic databases are valuable new tools that are assisting the FDA in its mission to promptly and efficiently review incoming submissions for regulatory approval of new food additives and food contact substances. The Center for Food Safety and Applied Nutrition's Office of Food Additive Safety (CFSAN/OFAS), in collaboration with Leadscope, Inc., is consolidating genetic toxicity data submitted in food additive petitions from the 1960s to the present day. The Center for Drug Evaluation and Research, Office of Pharmaceutical Science's Informatics and Computational Safety Analysis Staff (CDER/OPS/ICSAS) is separately gathering similar information from their submissions. Presently, these data are distributed in various locations such as paper files, microfiche, and non-standardized toxicology memoranda. The organization of the data into a consistent, searchable format will reduce paperwork, expedite the toxicology review process, and provide valuable information to industry that is currently available only to the FDA. Furthermore, by combining chemical structures with genetic toxicity information, biologically active moieties can be identified and used to develop quantitative structure-activity relationship (QSAR) modeling and testing guidelines. Additionally, chemicals devoid of toxicity data can be compared to known structures, allowing for improved safety review through the identification and analysis of structural analogs. Four database frameworks have been created: bacterial mutagenesis, in vitro chromosome aberration, in vitro mammalian mutagenesis, and in vivo micronucleus. Controlled vocabularies for these databases have been established. The four separate genetic toxicity databases are compiled into a single, structurally-searchable database for easy accessibility of the toxicity information. Beyond the genetic toxicity databases described here, additional databases for subchronic, chronic, and teratogenicity studies have been prepared

  4. Keyword Search in Databases

    CERN Document Server

    Yu, Jeffrey Xu; Chang, Lijun

    2009-01-01

    It has become highly desirable to provide users with flexible ways to query/search information over databases as simple as keyword search like Google search. This book surveys the recent developments on keyword search over databases, and focuses on finding structural information among objects in a database using a set of keywords. Such structural information to be returned can be either trees or subgraphs representing how the objects, that contain the required keywords, are interconnected in a relational database or in an XML database. The structural keyword search is completely different from

  5. THPdb: Database of FDA-approved peptide and protein therapeutics.

    Directory of Open Access Journals (Sweden)

    Salman Sadullah Usmani

    Full Text Available THPdb (http://crdd.osdd.net/raghava/thpdb/ is a manually curated repository of Food and Drug Administration (FDA approved therapeutic peptides and proteins. The information in THPdb has been compiled from 985 research publications, 70 patents and other resources like DrugBank. The current version of the database holds a total of 852 entries, providing comprehensive information on 239 US-FDA approved therapeutic peptides and proteins and their 380 drug variants. The information on each peptide and protein includes their sequences, chemical properties, composition, disease area, mode of activity, physical appearance, category or pharmacological class, pharmacodynamics, route of administration, toxicity, target of activity, etc. In addition, we have annotated the structure of most of the protein and peptides. A number of user-friendly tools have been integrated to facilitate easy browsing and data analysis. To assist scientific community, a web interface and mobile App have also been developed.

  6. FDA Acronyms and Abbreviations

    Data.gov (United States)

    U.S. Department of Health & Human Services — The FDA Acronyms and Abbreviations database provides a quick reference to acronyms and abbreviations related to Food and Drug Administration (FDA) activities

  7. BioCarian: search engine for exploratory searches in heterogeneous biological databases.

    Science.gov (United States)

    Zaki, Nazar; Tennakoon, Chandana

    2017-10-02

    There are a large number of biological databases publicly available for scientists in the web. Also, there are many private databases generated in the course of research projects. These databases are in a wide variety of formats. Web standards have evolved in the recent times and semantic web technologies are now available to interconnect diverse and heterogeneous sources of data. Therefore, integration and querying of biological databases can be facilitated by techniques used in semantic web. Heterogeneous databases can be converted into Resource Description Format (RDF) and queried using SPARQL language. Searching for exact queries in these databases is trivial. However, exploratory searches need customized solutions, especially when multiple databases are involved. This process is cumbersome and time consuming for those without a sufficient background in computer science. In this context, a search engine facilitating exploratory searches of databases would be of great help to the scientific community. We present BioCarian, an efficient and user-friendly search engine for performing exploratory searches on biological databases. The search engine is an interface for SPARQL queries over RDF databases. We note that many of the databases can be converted to tabular form. We first convert the tabular databases to RDF. The search engine provides a graphical interface based on facets to explore the converted databases. The facet interface is more advanced than conventional facets. It allows complex queries to be constructed, and have additional features like ranking of facet values based on several criteria, visually indicating the relevance of a facet value and presenting the most important facet values when a large number of choices are available. For the advanced users, SPARQL queries can be run directly on the databases. Using this feature, users will be able to incorporate federated searches of SPARQL endpoints. We used the search engine to do an exploratory search

  8. Fast Structural Search in Phylogenetic Databases

    Directory of Open Access Journals (Sweden)

    William H. Piel

    2005-01-01

    Full Text Available As the size of phylogenetic databases grows, the need for efficiently searching these databases arises. Thanks to previous and ongoing research, searching by attribute value and by text has become commonplace in these databases. However, searching by topological or physical structure, especially for large databases and especially for approximate matches, is still an art. We propose structural search techniques that, given a query or pattern tree P and a database of phylogenies D, find trees in D that are sufficiently close to P . The “closeness” is a measure of the topological relationships in P that are found to be the same or similar in a tree D in D. We develop a filtering technique that accelerates searches and present algorithms for rooted and unrooted trees where the trees can be weighted or unweighted. Experimental results on comparing the similarity measure with existing tree metrics and on evaluating the efficiency of the search techniques demonstrate that the proposed approach is promising

  9. Database Search Engines: Paradigms, Challenges and Solutions.

    Science.gov (United States)

    Verheggen, Kenneth; Martens, Lennart; Berven, Frode S; Barsnes, Harald; Vaudel, Marc

    2016-01-01

    The first step in identifying proteins from mass spectrometry based shotgun proteomics data is to infer peptides from tandem mass spectra, a task generally achieved using database search engines. In this chapter, the basic principles of database search engines are introduced with a focus on open source software, and the use of database search engines is demonstrated using the freely available SearchGUI interface. This chapter also discusses how to tackle general issues related to sequence database searching and shows how to minimize their impact.

  10. FDA Peanut-Containing Product Recall

    Data.gov (United States)

    U.S. Department of Health & Human Services — The FDA Peanut-Containing Product Recall widget allows you to browse the Food and Drug Administration (FDA) database of peanut butter and peanut-containing products...

  11. Interactive searching of facial image databases

    Science.gov (United States)

    Nicholls, Robert A.; Shepherd, John W.; Shepherd, Jean

    1995-09-01

    A set of psychological facial descriptors has been devised to enable computerized searching of criminal photograph albums. The descriptors have been used to encode image databased of up to twelve thousand images. Using a system called FACES, the databases are searched by translating a witness' verbal description into corresponding facial descriptors. Trials of FACES have shown that this coding scheme is more productive and efficient than searching traditional photograph albums. An alternative method of searching the encoded database using a genetic algorithm is currenly being tested. The genetic search method does not require the witness to verbalize a description of the target but merely to indicate a degree of similarity between the target and a limited selection of images from the database. The major drawback of FACES is that is requires a manual encoding of images. Research is being undertaken to automate the process, however, it will require an algorithm which can predict human descriptive values. Alternatives to human derived coding schemes exist using statistical classifications of images. Since databases encoded using statistical classifiers do not have an obvious direct mapping to human derived descriptors, a search method which does not require the entry of human descriptors is required. A genetic search algorithm is being tested for such a purpose.

  12. NBIC: Search Ballast Report Database

    Science.gov (United States)

    Smithsonian Environmental Research Center Logo US Coast Guard Logo Submit BW Report | Search NBIC Database developed an online database that can be queried through our website. Data are accessible for all coastal Lakes, have been incorporated into the NBIC database as of August 2004. Information on data availability

  13. FDA Adverse Event Reporting System (FAERS): Latest Quartely Data Files

    Data.gov (United States)

    U.S. Department of Health & Human Services — The FDA Adverse Event Reporting System (FAERS) is a database that contains information on adverse event and medication error reports submitted to FDA. The database...

  14. Trends in internet search activity, media coverage, and patient-centered health information after the FDA safety communications on surgical mesh for pelvic organ prolapse.

    Science.gov (United States)

    Stone, Benjamin V; Forde, James C; Levit, Valerie B; Lee, Richard K; Te, Alexis E; Chughtai, Bilal

    2016-11-01

    In July 2011, the US Food and Drug Administration (FDA) issued a safety communication regarding serious complications associated with surgical mesh for pelvic organ prolapse, prompting increased media and public attention. This study sought to analyze internet search activity and news article volume after this FDA warning and to evaluate the quality of websites providing patient-centered information. Google Trends™ was utilized to evaluate search engine trends for the term "pelvic organ prolapse" and associated terms between 1 January 2004 and 31 December 2014. Google News™ was utilized to quantify the number of news articles annually under the term "pelvic organ prolapse." The search results for the term "pelvic organ prolapse" were assessed for quality using the Health On the Net Foundation (HON) certification. There was a significant increase in search activity from 37.42 in 2010 to 57.75 in 2011, at the time of the FDA communication (p = 0.021). No other annual interval had a statistically significant increase in search activity. The single highest monthly search activity, given the value of 100, was August 2011, immediately following the July 2011 notification, with the next highest value being 98 in July 2011. Linear regression analysis of news articles per year since the FDA communication revealed r 2  = 0.88, with a coefficient of 186. Quality assessment demonstrated that 42 % of websites were HON-certified, with .gov sites providing the highest quality information. Although the 2011 FDA safety communication on surgical mesh was associated with increased public and media attention, the quality of relevant health information on the internet remains of poor quality. Future quality assurance measures may be critical in enabling patients to play active roles in their own healthcare.

  15. Search pattern of databases by the undergraduate students of ...

    African Journals Online (AJOL)

    The main objective of this study is to assess the awareness and search pattern of databases in order to determine the extent to which user are aware and search for databases by examining the relationship between their Awareness and search patterns of Databases, and their information literacy skills. The methodology ...

  16. FDA Recognized Consensus Standards

    Data.gov (United States)

    U.S. Department of Health & Human Services — This database consists of those national and international standards recognized by FDA which manufacturers can declare conformity to and is part of the information...

  17. FDA Drug Label Data

    Data.gov (United States)

    U.S. Department of Health & Human Services — This file contains the data elements used for searching the FDA Online Data Repository including proprietary name, active ingredients, marketing application number...

  18. Using SQL Databases for Sequence Similarity Searching and Analysis.

    Science.gov (United States)

    Pearson, William R; Mackey, Aaron J

    2017-09-13

    Relational databases can integrate diverse types of information and manage large sets of similarity search results, greatly simplifying genome-scale analyses. By focusing on taxonomic subsets of sequences, relational databases can reduce the size and redundancy of sequence libraries and improve the statistical significance of homologs. In addition, by loading similarity search results into a relational database, it becomes possible to explore and summarize the relationships between all of the proteins in an organism and those in other biological kingdoms. This unit describes how to use relational databases to improve the efficiency of sequence similarity searching and demonstrates various large-scale genomic analyses of homology-related data. It also describes the installation and use of a simple protein sequence database, seqdb_demo, which is used as a basis for the other protocols. The unit also introduces search_demo, a database that stores sequence similarity search results. The search_demo database is then used to explore the evolutionary relationships between E. coli proteins and proteins in other organisms in a large-scale comparative genomic analysis. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

  19. Molecule database framework: a framework for creating database applications with chemical structure search capability.

    Science.gov (United States)

    Kiener, Joos

    2013-12-11

    Research in organic chemistry generates samples of novel chemicals together with their properties and other related data. The involved scientists must be able to store this data and search it by chemical structure. There are commercial solutions for common needs like chemical registration systems or electronic lab notebooks. However for specific requirements of in-house databases and processes no such solutions exist. Another issue is that commercial solutions have the risk of vendor lock-in and may require an expensive license of a proprietary relational database management system. To speed up and simplify the development for applications that require chemical structure search capabilities, I have developed Molecule Database Framework. The framework abstracts the storing and searching of chemical structures into method calls. Therefore software developers do not require extensive knowledge about chemistry and the underlying database cartridge. This decreases application development time. Molecule Database Framework is written in Java and I created it by integrating existing free and open-source tools and frameworks. The core functionality includes:•Support for multi-component compounds (mixtures)•Import and export of SD-files•Optional security (authorization)For chemical structure searching Molecule Database Framework leverages the capabilities of the Bingo Cartridge for PostgreSQL and provides type-safe searching, caching, transactions and optional method level security. Molecule Database Framework supports multi-component chemical compounds (mixtures).Furthermore the design of entity classes and the reasoning behind it are explained. By means of a simple web application I describe how the framework could be used. I then benchmarked this example application to create some basic performance expectations for chemical structure searches and import and export of SD-files. By using a simple web application it was shown that Molecule Database Framework

  20. PubData: search engine for bioinformatics databases worldwide

    OpenAIRE

    Vand, Kasra; Wahlestedt, Thor; Khomtchouk, Kelly; Sayed, Mohammed; Wahlestedt, Claes; Khomtchouk, Bohdan

    2016-01-01

    We propose a search engine and file retrieval system for all bioinformatics databases worldwide. PubData searches biomedical data in a user-friendly fashion similar to how PubMed searches biomedical literature. PubData is built on novel network programming, natural language processing, and artificial intelligence algorithms that can patch into the file transfer protocol servers of any user-specified bioinformatics database, query its contents, retrieve files for download, and adapt to the use...

  1. MetaboSearch: tool for mass-based metabolite identification using multiple databases.

    Directory of Open Access Journals (Sweden)

    Bin Zhou

    Full Text Available Searching metabolites against databases according to their masses is often the first step in metabolite identification for a mass spectrometry-based untargeted metabolomics study. Major metabolite databases include Human Metabolome DataBase (HMDB, Madison Metabolomics Consortium Database (MMCD, Metlin, and LIPID MAPS. Since each one of these databases covers only a fraction of the metabolome, integration of the search results from these databases is expected to yield a more comprehensive coverage. However, the manual combination of multiple search results is generally difficult when identification of hundreds of metabolites is desired. We have implemented a web-based software tool that enables simultaneous mass-based search against the four major databases, and the integration of the results. In addition, more complete chemical identifier information for the metabolites is retrieved by cross-referencing multiple databases. The search results are merged based on IUPAC International Chemical Identifier (InChI keys. Besides a simple list of m/z values, the software can accept the ion annotation information as input for enhanced metabolite identification. The performance of the software is demonstrated on mass spectrometry data acquired in both positive and negative ionization modes. Compared with search results from individual databases, MetaboSearch provides better coverage of the metabolome and more complete chemical identifier information.The software tool is available at http://omics.georgetown.edu/MetaboSearch.html.

  2. Quantum search of a real unstructured database

    Science.gov (United States)

    Broda, Bogusław

    2016-02-01

    A simple circuit implementation of the oracle for Grover's quantum search of a real unstructured classical database is proposed. The oracle contains a kind of quantumly accessible classical memory, which stores the database.

  3. The Development of a Combined Search for a Heterogeneous Chemistry Database

    Directory of Open Access Journals (Sweden)

    Lulu Jiang

    2015-05-01

    Full Text Available A combined search, which joins a slow molecule structure search with a fast compound property search, results in more accurate search results and has been applied in several chemistry databases. However, the problems of search speed differences and combining the two separate search results are two major challenges. In this paper, two kinds of search strategies, synchronous search and asynchronous search, are proposed to solve these problems in the heterogeneous structure database and the property database found in ChemDB, a chemistry database owned by the Institute of Process Engineering, CAS. Their advantages and disadvantages under different conditions are discussed in detail. Furthermore, we applied these two searches to ChemDB and used them to screen for potential molecules that can work as CO2 absorbents. The results reveal that this combined search discovers reasonable target molecules within an acceptable time frame.

  4. Searching Harvard Business Review Online. . . Lessons in Searching a Full Text Database.

    Science.gov (United States)

    Tenopir, Carol

    1985-01-01

    This article examines the Harvard Business Review Online (HBRO) database (bibliographic description fields, abstracts, extracted information, full text, subject descriptors) and reports on 31 sample HBRO searches conducted in Bibliographic Retrieval Services to test differences between searching full text and searching bibliographic record. Sample…

  5. muBLASTP: database-indexed protein sequence search on multicore CPUs.

    Science.gov (United States)

    Zhang, Jing; Misra, Sanchit; Wang, Hao; Feng, Wu-Chun

    2016-11-04

    The Basic Local Alignment Search Tool (BLAST) is a fundamental program in the life sciences that searches databases for sequences that are most similar to a query sequence. Currently, the BLAST algorithm utilizes a query-indexed approach. Although many approaches suggest that sequence search with a database index can achieve much higher throughput (e.g., BLAT, SSAHA, and CAFE), they cannot deliver the same level of sensitivity as the query-indexed BLAST, i.e., NCBI BLAST, or they can only support nucleotide sequence search, e.g., MegaBLAST. Due to different challenges and characteristics between query indexing and database indexing, the existing techniques for query-indexed search cannot be used into database indexed search. muBLASTP, a novel database-indexed BLAST for protein sequence search, delivers identical hits returned to NCBI BLAST. On Intel Haswell multicore CPUs, for a single query, the single-threaded muBLASTP achieves up to a 4.41-fold speedup for alignment stages, and up to a 1.75-fold end-to-end speedup over single-threaded NCBI BLAST. For a batch of queries, the multithreaded muBLASTP achieves up to a 5.7-fold speedups for alignment stages, and up to a 4.56-fold end-to-end speedup over multithreaded NCBI BLAST. With a newly designed index structure for protein database and associated optimizations in BLASTP algorithm, we re-factored BLASTP algorithm for modern multicore processors that achieves much higher throughput with acceptable memory footprint for the database index.

  6. Searching mixed DNA profiles directly against profile databases.

    Science.gov (United States)

    Bright, Jo-Anne; Taylor, Duncan; Curran, James; Buckleton, John

    2014-03-01

    DNA databases have revolutionised forensic science. They are a powerful investigative tool as they have the potential to identify persons of interest in criminal investigations. Routinely, a DNA profile generated from a crime sample could only be searched for in a database of individuals if the stain was from single contributor (single source) or if a contributor could unambiguously be determined from a mixed DNA profile. This meant that a significant number of samples were unsuitable for database searching. The advent of continuous methods for the interpretation of DNA profiles offers an advanced way to draw inferential power from the considerable investment made in DNA databases. Using these methods, each profile on the database may be considered a possible contributor to a mixture and a likelihood ratio (LR) can be formed. Those profiles which produce a sufficiently large LR can serve as an investigative lead. In this paper empirical studies are described to determine what constitutes a large LR. We investigate the effect on a database search of complex mixed DNA profiles with contributors in equal proportions with dropout as a consideration, and also the effect of an incorrect assignment of the number of contributors to a profile. In addition, we give, as a demonstration of the method, the results using two crime samples that were previously unsuitable for database comparison. We show that effective management of the selection of samples for searching and the interpretation of the output can be highly informative. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  7. MICA: desktop software for comprehensive searching of DNA databases

    Directory of Open Access Journals (Sweden)

    Glick Benjamin S

    2006-10-01

    Full Text Available Abstract Background Molecular biologists work with DNA databases that often include entire genomes. A common requirement is to search a DNA database to find exact matches for a nondegenerate or partially degenerate query. The software programs available for such purposes are normally designed to run on remote servers, but an appealing alternative is to work with DNA databases stored on local computers. We describe a desktop software program termed MICA (K-Mer Indexing with Compact Arrays that allows large DNA databases to be searched efficiently using very little memory. Results MICA rapidly indexes a DNA database. On a Macintosh G5 computer, the complete human genome could be indexed in about 5 minutes. The indexing algorithm recognizes all 15 characters of the DNA alphabet and fully captures the information in any DNA sequence, yet for a typical sequence of length L, the index occupies only about 2L bytes. The index can be searched to return a complete list of exact matches for a nondegenerate or partially degenerate query of any length. A typical search of a long DNA sequence involves reading only a small fraction of the index into memory. As a result, searches are fast even when the available RAM is limited. Conclusion MICA is suitable as a search engine for desktop DNA analysis software.

  8. An approach in building a chemical compound search engine in oracle database.

    Science.gov (United States)

    Wang, H; Volarath, P; Harrison, R

    2005-01-01

    A searching or identifying of chemical compounds is an important process in drug design and in chemistry research. An efficient search engine involves a close coupling of the search algorithm and database implementation. The database must process chemical structures, which demands the approaches to represent, store, and retrieve structures in a database system. In this paper, a general database framework for working as a chemical compound search engine in Oracle database is described. The framework is devoted to eliminate data type constrains for potential search algorithms, which is a crucial step toward building a domain specific query language on top of SQL. A search engine implementation based on the database framework is also demonstrated. The convenience of the implementation emphasizes the efficiency and simplicity of the framework.

  9. Searching the ASRS Database Using QUORUM Keyword Search, Phrase Search, Phrase Generation, and Phrase Discovery

    Science.gov (United States)

    McGreevy, Michael W.; Connors, Mary M. (Technical Monitor)

    2001-01-01

    To support Search Requests and Quick Responses at the Aviation Safety Reporting System (ASRS), four new QUORUM methods have been developed: keyword search, phrase search, phrase generation, and phrase discovery. These methods build upon the core QUORUM methods of text analysis, modeling, and relevance-ranking. QUORUM keyword search retrieves ASRS incident narratives that contain one or more user-specified keywords in typical or selected contexts, and ranks the narratives on their relevance to the keywords in context. QUORUM phrase search retrieves narratives that contain one or more user-specified phrases, and ranks the narratives on their relevance to the phrases. QUORUM phrase generation produces a list of phrases from the ASRS database that contain a user-specified word or phrase. QUORUM phrase discovery finds phrases that are related to topics of interest. Phrase generation and phrase discovery are particularly useful for finding query phrases for input to QUORUM phrase search. The presentation of the new QUORUM methods includes: a brief review of the underlying core QUORUM methods; an overview of the new methods; numerous, concrete examples of ASRS database searches using the new methods; discussion of related methods; and, in the appendices, detailed descriptions of the new methods.

  10. When is a search not a search? A comparison of searching the AMED complementary health database via EBSCOhost, OVID and DIALOG.

    Science.gov (United States)

    Younger, Paula; Boddy, Kate

    2009-06-01

    The researchers involved in this study work at Exeter Health library and at the Complementary Medicine Unit, Peninsula School of Medicine and Dentistry (PCMD). Within this collaborative environment it is possible to access the electronic resources of three institutions. This includes access to AMED and other databases using different interfaces. The aim of this study was to investigate whether searching different interfaces to the AMED allied health and complementary medicine database produced the same results when using identical search terms. The following Internet-based AMED interfaces were searched: DIALOG DataStar; EBSCOhost and OVID SP_UI01.00.02. Search results from all three databases were saved in an endnote database to facilitate analysis. A checklist was also compiled comparing interface features. In our initial search, DIALOG returned 29 hits, OVID 14 and Ebsco 8. If we assume that DIALOG returned 100% of potential hits, OVID initially returned only 48% of hits and EBSCOhost only 28%. In our search, a researcher using the Ebsco interface to carry out a simple search on AMED would miss over 70% of possible search hits. Subsequent EBSCOhost searches on different subjects failed to find between 21 and 86% of the hits retrieved using the same keywords via DIALOG DataStar. In two cases, the simple EBSCOhost search failed to find any of the results found via DIALOG DataStar. Depending on the interface, the number of hits retrieved from the same database with the same simple search can vary dramatically. Some simple searches fail to retrieve a substantial percentage of citations. This may result in an uninformed literature review, research funding application or treatment intervention. In addition to ensuring that keywords, spelling and medical subject headings (MeSH) accurately reflect the nature of the search, database users should include wildcards and truncation and adapt their search strategy substantially to retrieve the maximum number of appropriate

  11. Phonetic search methods for large speech databases

    CERN Document Server

    Moyal, Ami; Tetariy, Ella; Gishri, Michal

    2013-01-01

    “Phonetic Search Methods for Large Databases” focuses on Keyword Spotting (KWS) within large speech databases. The brief will begin by outlining the challenges associated with Keyword Spotting within large speech databases using dynamic keyword vocabularies. It will then continue by highlighting the various market segments in need of KWS solutions, as well as, the specific requirements of each market segment. The work also includes a detailed description of the complexity of the task and the different methods that are used, including the advantages and disadvantages of each method and an in-depth comparison. The main focus will be on the Phonetic Search method and its efficient implementation. This will include a literature review of the various methods used for the efficient implementation of Phonetic Search Keyword Spotting, with an emphasis on the authors’ own research which entails a comparative analysis of the Phonetic Search method which includes algorithmic details. This brief is useful for resea...

  12. Optimal database combinations for literature searches in systematic reviews : a prospective exploratory study

    NARCIS (Netherlands)

    Bramer, W. M.; Rethlefsen, Melissa L.; Kleijnen, Jos; Franco, Oscar H.

    2017-01-01

    Background: Within systematic reviews, when searching for relevant references, it is advisable to use multiple databases. However, searching databases is laborious and time-consuming, as syntax of search strategies are database specific. We aimed to determine the optimal combination of databases

  13. Method and electronic database search engine for exposing the content of an electronic database

    NARCIS (Netherlands)

    Stappers, P.J.

    2000-01-01

    The invention relates to an electronic database search engine comprising an electronic memory device suitable for storing and releasing elements from the database, a display unit, a user interface for selecting and displaying at least one element from the database on the display unit, and control

  14. Protein structure database search and evolutionary classification.

    Science.gov (United States)

    Yang, Jinn-Moon; Tung, Chi-Hua

    2006-01-01

    As more protein structures become available and structural genomics efforts provide structural models in a genome-wide strategy, there is a growing need for fast and accurate methods for discovering homologous proteins and evolutionary classifications of newly determined structures. We have developed 3D-BLAST, in part, to address these issues. 3D-BLAST is as fast as BLAST and calculates the statistical significance (E-value) of an alignment to indicate the reliability of the prediction. Using this method, we first identified 23 states of the structural alphabet that represent pattern profiles of the backbone fragments and then used them to represent protein structure databases as structural alphabet sequence databases (SADB). Our method enhanced BLAST as a search method, using a new structural alphabet substitution matrix (SASM) to find the longest common substructures with high-scoring structured segment pairs from an SADB database. Using personal computers with Intel Pentium4 (2.8 GHz) processors, our method searched more than 10 000 protein structures in 1.3 s and achieved a good agreement with search results from detailed structure alignment methods. [3D-BLAST is available at http://3d-blast.life.nctu.edu.tw].

  15. An experimental investigation of masking in the US FDA adverse event reporting system database.

    Science.gov (United States)

    Wang, Hsin-wei; Hochberg, Alan M; Pearson, Ronald K; Hauben, Manfred

    2010-12-01

    A phenomenon of 'masking' or 'cloaking' in pharmacovigilance data mining has been described, which can potentially cause signals of disproportionate reporting (SDRs) to be missed, particularly in pharmaceutical company databases. Masking has been predicted theoretically, observed anecdotally or studied to a limited extent in both pharmaceutical company and health authority databases, but no previous publication systematically assesses its occurrence in a large health authority database. To explore the nature, extent and possible consequences of masking in the US FDA Adverse Event Reporting System (AERS) database by applying various experimental unmasking protocols to a set of drugs and events representing realistic pharmacovigilance analysis conditions. This study employed AERS data from 2001 through 2005. For a set of 63 Medical Dictionary for Regulatory Activities (MedDRA®) Preferred Terms (PTs), disproportionality analysis was carried out with respect to all drugs included in the AERS database, using a previously described urn-model-based algorithm. We specifically sought masking in which drug removal induced an increase in the statistical representation of a drug-event combination (DEC) that resulted in the emergence of a new SDR. We performed a series of unmasking experiments selecting drugs for removal using rational statistical decision rules based on the requirement of a reporting ratio (RR) >1, top-ranked statistical unexpectedness (SU) and relatedness as reflected in the WHO Anatomical Therapeutic Chemical level 4 (ATC4) grouping. In order to assess the possible extent of residual masking we performed two supplemental purely empirical analyses on a limited subset of data. This entailed testing every drug and drug group to determine which was most influential in uncovering masked SDRs. We assessed the strength of external evidence for a causal association for a small number of masked SDRs involving a subset of 29 drugs for which level of evidence

  16. Forensic utilization of familial searches in DNA databases.

    Science.gov (United States)

    Gershaw, Cassandra J; Schweighardt, Andrew J; Rourke, Linda C; Wallace, Margaret M

    2011-01-01

    DNA evidence is widely recognized as an invaluable tool in the process of investigation and identification, as well as one of the most sought after types of evidence for presentation to a jury. In the United States, the development of state and federal DNA databases has greatly impacted the forensic community by creating an efficient, searchable system that can be used to eliminate or include suspects in an investigation based on matching DNA profiles - the profile already in the database to the profile of the unknown sample in evidence. Recent changes in legislation have begun to allow for the possibility to expand the parameters of DNA database searches, taking into account the possibility of familial searches. This article discusses prospective positive outcomes of utilizing familial DNA searches and acknowledges potential negative outcomes, thereby presenting both sides of this very complicated, rapidly evolving situation. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

  17. MIDAS: a database-searching algorithm for metabolite identification in metabolomics.

    Science.gov (United States)

    Wang, Yingfeng; Kora, Guruprasad; Bowen, Benjamin P; Pan, Chongle

    2014-10-07

    A database searching approach can be used for metabolite identification in metabolomics by matching measured tandem mass spectra (MS/MS) against the predicted fragments of metabolites in a database. Here, we present the open-source MIDAS algorithm (Metabolite Identification via Database Searching). To evaluate a metabolite-spectrum match (MSM), MIDAS first enumerates possible fragments from a metabolite by systematic bond dissociation, then calculates the plausibility of the fragments based on their fragmentation pathways, and finally scores the MSM to assess how well the experimental MS/MS spectrum from collision-induced dissociation (CID) is explained by the metabolite's predicted CID MS/MS spectrum. MIDAS was designed to search high-resolution tandem mass spectra acquired on time-of-flight or Orbitrap mass spectrometer against a metabolite database in an automated and high-throughput manner. The accuracy of metabolite identification by MIDAS was benchmarked using four sets of standard tandem mass spectra from MassBank. On average, for 77% of original spectra and 84% of composite spectra, MIDAS correctly ranked the true compounds as the first MSMs out of all MetaCyc metabolites as decoys. MIDAS correctly identified 46% more original spectra and 59% more composite spectra at the first MSMs than an existing database-searching algorithm, MetFrag. MIDAS was showcased by searching a published real-world measurement of a metabolome from Synechococcus sp. PCC 7002 against the MetaCyc metabolite database. MIDAS identified many metabolites missed in the previous study. MIDAS identifications should be considered only as candidate metabolites, which need to be confirmed using standard compounds. To facilitate manual validation, MIDAS provides annotated spectra for MSMs and labels observed mass spectral peaks with predicted fragments. The database searching and manual validation can be performed online at http://midas.omicsbio.org.

  18. WGDB: Wood Gene Database with search interface.

    Science.gov (United States)

    Goyal, Neha; Ginwal, H S

    2014-01-01

    Wood quality can be defined in terms of particular end use with the involvement of several traits. Over the last fifteen years researchers have assessed the wood quality traits in forest trees. The wood quality was categorized as: cell wall biochemical traits, fibre properties include the microfibril angle, density and stiffness in loblolly pine [1]. The user friendly and an open-access database has been developed named Wood Gene Database (WGDB) for describing the wood genes along the information of protein and published research articles. It contains 720 wood genes from species namely Pinus, Deodar, fast growing trees namely Poplar, Eucalyptus. WGDB designed to encompass the majority of publicly accessible genes codes for cellulose, hemicellulose and lignin in tree species which are responsive to wood formation and quality. It is an interactive platform for collecting, managing and searching the specific wood genes; it also enables the data mining relate to the genomic information specifically in Arabidopsis thaliana, Populus trichocarpa, Eucalyptus grandis, Pinus taeda, Pinus radiata, Cedrus deodara, Cedrus atlantica. For user convenience, this database is cross linked with public databases namely NCBI, EMBL & Dendrome with the search engine Google for making it more informative and provides bioinformatics tools named BLAST,COBALT. The database is freely available on www.wgdb.in.

  19. Two Search Techniques within a Human Pedigree Database

    OpenAIRE

    Gersting, J. M.; Conneally, P. M.; Rogers, K.

    1982-01-01

    This paper presents the basic features of two search techniques from MEGADATS-2 (MEdical Genetics Acquisition and DAta Transfer System), a system for collecting, storing, retrieving and plotting human family pedigrees. The individual search provides a quick method for locating an individual in the pedigree database. This search uses a modified soundex coding and an inverted file structure based on a composite key. The navigational search uses a set of pedigree traversal operations (individual...

  20. FDA-approved drugs that are spermatotoxic in animals and the utility of animal testing for human risk prediction.

    Science.gov (United States)

    Rayburn, Elizabeth R; Gao, Liang; Ding, Jiayi; Ding, Hongxia; Shao, Jun; Li, Haibo

    2018-02-01

    This study reviews FDA-approved drugs that negatively impact spermatozoa in animals, as well as how these findings reflect on observations in human male gametes. The FDA drug warning labels included in the DailyMed database and the peer-reviewed literature in the PubMed database were searched for information to identify single-ingredient, FDA-approved prescription drugs with spermatotoxic effects. A total of 235 unique, single-ingredient, FDA-approved drugs reported to be spermatotoxic in animals were identified in the drug labels. Forty-nine of these had documented negative effects on humans in either the drug label or literature, while 31 had no effect or a positive impact on human sperm. For the other 155 drugs that were spermatotoxic in animals, no human data was available. The current animal models are not very effective for predicting human spermatotoxicity, and there is limited information available about the impact of many drugs on human spermatozoa. New approaches should be designed that more accurately reflect the findings in men, including more studies on human sperm in vitro and studies using other systems (ex vivo tissue culture, xenograft models, in silico studies, etc.). In addition, the present data is often incomplete or reported in a manner that prevents interpretation of their clinical relevance. Changes should be made to the requirements for pre-clinical testing, drug surveillance, and the warning labels of drugs to ensure that the potential risks to human fertility are clearly indicated.

  1. Mining FDA drug labels for medical conditions.

    Science.gov (United States)

    Li, Qi; Deleger, Louise; Lingren, Todd; Zhai, Haijun; Kaiser, Megan; Stoutenborough, Laura; Jegga, Anil G; Cohen, Kevin Bretonnel; Solti, Imre

    2013-04-24

    Cincinnati Children's Hospital Medical Center (CCHMC) has built the initial Natural Language Processing (NLP) component to extract medications with their corresponding medical conditions (Indications, Contraindications, Overdosage, and Adverse Reactions) as triples of medication-related information ([(1) drug name]-[(2) medical condition]-[(3) LOINC section header]) for an intelligent database system, in order to improve patient safety and the quality of health care. The Food and Drug Administration's (FDA) drug labels are used to demonstrate the feasibility of building the triples as an intelligent database system task. This paper discusses a hybrid NLP system, called AutoMCExtractor, to collect medical conditions (including disease/disorder and sign/symptom) from drug labels published by the FDA. Altogether, 6,611 medical conditions in a manually-annotated gold standard were used for the system evaluation. The pre-processing step extracted the plain text from XML file and detected eight related LOINC sections (e.g. Adverse Reactions, Warnings and Precautions) for medical condition extraction. Conditional Random Fields (CRF) classifiers, trained on token, linguistic, and semantic features, were then used for medical condition extraction. Lastly, dictionary-based post-processing corrected boundary-detection errors of the CRF step. We evaluated the AutoMCExtractor on manually-annotated FDA drug labels and report the results on both token and span levels. Precision, recall, and F-measure were 0.90, 0.81, and 0.85, respectively, for the span level exact match; for the token-level evaluation, precision, recall, and F-measure were 0.92, 0.73, and 0.82, respectively. The results demonstrate that (1) medical conditions can be extracted from FDA drug labels with high performance; and (2) it is feasible to develop a framework for an intelligent database system.

  2. Archiving, ordering and searching: search engines, algorithms, databases and deep mediatization

    DEFF Research Database (Denmark)

    Andersen, Jack

    2018-01-01

    This article argues that search engines, algorithms, and databases can be considered as a way of understanding deep mediatization (Couldry & Hepp, 2016). They are embedded in a variety of social and cultural practices and as such they change our communicative actions to be shaped by their logic o...... reviewed recent trends in mediatization research, the argument is discussed and unfolded in-between the material and social constructivist-phenomenological interpretations of mediatization. In conclusion, it is discussed how deep this form of mediatization can be taken to be.......This article argues that search engines, algorithms, and databases can be considered as a way of understanding deep mediatization (Couldry & Hepp, 2016). They are embedded in a variety of social and cultural practices and as such they change our communicative actions to be shaped by their logic...

  3. Search Databases and Statistics

    DEFF Research Database (Denmark)

    Refsgaard, Jan C; Munk, Stephanie; Jensen, Lars J

    2016-01-01

    having strengths and weaknesses that must be considered for the individual needs. These are reviewed in this chapter. Equally critical for generating highly confident output datasets is the application of sound statistical criteria to limit the inclusion of incorrect peptide identifications from database...... searches. Additionally, careful filtering and use of appropriate statistical tests on the output datasets affects the quality of all downstream analyses and interpretation of the data. Our considerations and general practices on these aspects of phosphoproteomics data processing are presented here....

  4. A practical approach for inexpensive searches of radiology report databases.

    Science.gov (United States)

    Desjardins, Benoit; Hamilton, R Curtis

    2007-06-01

    We present a method to perform full text searches of radiology reports for the large number of departments that do not have this ability as part of their radiology or hospital information system. A tool written in Microsoft Access (front-end) has been designed to search a server (back-end) containing the indexed backup weekly copy of the full relational database extracted from a radiology information system (RIS). This front end-/back-end approach has been implemented in a large academic radiology department, and is used for teaching, research and administrative purposes. The weekly second backup of the 80 GB, 4 million record RIS database takes 2 hours. Further indexing of the exported radiology reports takes 6 hours. Individual searches of the indexed database typically take less than 1 minute on the indexed database and 30-60 minutes on the nonindexed database. Guidelines to properly address privacy and institutional review board issues are closely followed by all users. This method has potential to improve teaching, research, and administrative programs within radiology departments that cannot afford more expensive technology.

  5. Sagace: A web-based search engine for biomedical databases in Japan

    Directory of Open Access Journals (Sweden)

    Morita Mizuki

    2012-10-01

    Full Text Available Abstract Background In the big data era, biomedical research continues to generate a large amount of data, and the generated information is often stored in a database and made publicly available. Although combining data from multiple databases should accelerate further studies, the current number of life sciences databases is too large to grasp features and contents of each database. Findings We have developed Sagace, a web-based search engine that enables users to retrieve information from a range of biological databases (such as gene expression profiles and proteomics data and biological resource banks (such as mouse models of disease and cell lines. With Sagace, users can search more than 300 databases in Japan. Sagace offers features tailored to biomedical research, including manually tuned ranking, a faceted navigation to refine search results, and rich snippets constructed with retrieved metadata for each database entry. Conclusions Sagace will be valuable for experts who are involved in biomedical research and drug development in both academia and industry. Sagace is freely available at http://sagace.nibio.go.jp/en/.

  6. Audio stream classification for multimedia database search

    Science.gov (United States)

    Artese, M.; Bianco, S.; Gagliardi, I.; Gasparini, F.

    2013-03-01

    Search and retrieval of huge archives of Multimedia data is a challenging task. A classification step is often used to reduce the number of entries on which to perform the subsequent search. In particular, when new entries of the database are continuously added, a fast classification based on simple threshold evaluation is desirable. In this work we present a CART-based (Classification And Regression Tree [1]) classification framework for audio streams belonging to multimedia databases. The database considered is the Archive of Ethnography and Social History (AESS) [2], which is mainly composed of popular songs and other audio records describing the popular traditions handed down generation by generation, such as traditional fairs, and customs. The peculiarities of this database are that it is continuously updated; the audio recordings are acquired in unconstrained environment; and for the non-expert human user is difficult to create the ground truth labels. In our experiments, half of all the available audio files have been randomly extracted and used as training set. The remaining ones have been used as test set. The classifier has been trained to distinguish among three different classes: speech, music, and song. All the audio files in the dataset have been previously manually labeled into the three classes above defined by domain experts.

  7. The LAILAPS Search Engine: Relevance Ranking in Life Science Databases

    Directory of Open Access Journals (Sweden)

    Lange Matthias

    2010-06-01

    Full Text Available Search engines and retrieval systems are popular tools at a life science desktop. The manual inspection of hundreds of database entries, that reflect a life science concept or fact, is a time intensive daily work. Hereby, not the number of query results matters, but the relevance does. In this paper, we present the LAILAPS search engine for life science databases. The concept is to combine a novel feature model for relevance ranking, a machine learning approach to model user relevance profiles, ranking improvement by user feedback tracking and an intuitive and slim web user interface, that estimates relevance rank by tracking user interactions. Queries are formulated as simple keyword lists and will be expanded by synonyms. Supporting a flexible text index and a simple data import format, LAILAPS can easily be used both as search engine for comprehensive integrated life science databases and for small in-house project databases.

  8. Simplified validation of borderline hits of database searches

    OpenAIRE

    Thomas, Henrik; Shevchenko, Andrej

    2008-01-01

    Along with unequivocal hits produced by matching multiple MS/MS spectra to database sequences, LC-MS/MS analysis often yields a large number of hits of borderline statistical confidence. To simplify their validation, we propose to use rapid de novo interpretation of all acquired MS/MS spectra and, with the help of a simple software tool, display the candidate sequences together with each database search hit. We demonstrate that comparing hit database sequences and independent de novo interpre...

  9. Database searches for qualitative research

    OpenAIRE

    Evans, David

    2002-01-01

    Interest in the role of qualitative research in evidence-based health care is growing. However, the methods currently used to identify quantitative research do not translate easily to qualitative research. This paper highlights some of the difficulties during searches of electronic databases for qualitative research. These difficulties relate to the descriptive nature of the titles used in some qualitative studies, the variable information provided in abstracts, and the differences in the ind...

  10. A Web-based Tool for SDSS and 2MASS Database Searches

    Science.gov (United States)

    Hendrickson, M. A.; Uomoto, A.; Golimowski, D. A.

    We have developed a web site using HTML, Php, Python, and MySQL that extracts, processes, and displays data from the Sloan Digital Sky Survey (SDSS) and the Two-Micron All-Sky Survey (2MASS). The goal is to locate brown dwarf candidates in the SDSS database by looking at color cuts; however, this site could also be useful for targeted searches of other databases as well. MySQL databases are created from broad searches of SDSS and 2MASS data. Broad queries on the SDSS and 2MASS database servers are run weekly so that observers have the most up-to-date information from which to select candidates for observation. Observers can look at detailed information about specific objects including finding charts, images, and available spectra. In addition, updates from previous observations can be added by any collaborators; this format makes observational collaboration simple. Observers can also restrict the database search, just before or during an observing run, to select objects of special interest.

  11. Using relational databases for improved sequence similarity searching and large-scale genomic analyses.

    Science.gov (United States)

    Mackey, Aaron J; Pearson, William R

    2004-10-01

    Relational databases are designed to integrate diverse types of information and manage large sets of search results, greatly simplifying genome-scale analyses. Relational databases are essential for management and analysis of large-scale sequence analyses, and can also be used to improve the statistical significance of similarity searches by focusing on subsets of sequence libraries most likely to contain homologs. This unit describes using relational databases to improve the efficiency of sequence similarity searching and to demonstrate various large-scale genomic analyses of homology-related data. This unit describes the installation and use of a simple protein sequence database, seqdb_demo, which is used as a basis for the other protocols. These include basic use of the database to generate a novel sequence library subset, how to extend and use seqdb_demo for the storage of sequence similarity search results and making use of various kinds of stored search results to address aspects of comparative genomic analysis.

  12. Federated or cached searches: providing expected performance from multiple invasive species databases

    Science.gov (United States)

    Graham, Jim; Jarnevich, Catherine S.; Simpson, Annie; Newman, Gregory J.; Stohlgren, Thomas J.

    2011-01-01

    Invasive species are a universal global problem, but the information to identify them, manage them, and prevent invasions is stored around the globe in a variety of formats. The Global Invasive Species Information Network is a consortium of organizations working toward providing seamless access to these disparate databases via the Internet. A distributed network of databases can be created using the Internet and a standard web service protocol. There are two options to provide this integration. First, federated searches are being proposed to allow users to search “deep” web documents such as databases for invasive species. A second method is to create a cache of data from the databases for searching. We compare these two methods, and show that federated searches will not provide the performance and flexibility required from users and a central cache of the datum are required to improve performance.

  13. Searching Databases without Query-Building Aids: Implications for Dyslexic Users

    Science.gov (United States)

    Berget, Gerd; Sandnes, Frode Eika

    2015-01-01

    Introduction: Few studies document the information searching behaviour of users with cognitive impairments. This paper therefore addresses the effect of dyslexia on information searching in a database with no tolerance for spelling errors and no query-building aids. The purpose was to identify effective search interface design guidelines that…

  14. Students are Confident Using Federated Search Tools as much as Single Databases. A Review of: Armstrong, A. (2009. Student perceptions of federated searching vs. single database searching. Reference Services Review, 37(3, 291-303. doi:10.1108/00907320910982785

    Directory of Open Access Journals (Sweden)

    Deena Yanofsky

    2011-09-01

    Full Text Available Objective – To measure students’ perceptions of the ease-of-use and efficacy of a federated search tool versus a single multidisciplinary database.Design – An evaluation worksheet, employing a combination of quantitative and qualitative questions.Setting – A required, first-year English composition course taught at the University of Illinois at Chicago (UIC.Subjects – Thirty-one undergraduate students completed and submitted the worksheet.Methods – Students attended two library instruction sessions. The first session introduced participants to basic Boolean searching (using AND only, selecting appropriate keywords and searching for books in the library catalogue. In the second library session, students were handed an evaluation worksheet and, with no introduction to the process of searching article databases, were asked to find relevant articles on a research topic of their own choosing using both a federated search tool and a single multidisciplinary database. The evaluation worksheet was divided into four sections: step-by-step instructions for accessing the single multidisciplinary database and the federated search tool; space to record search strings in both resources; space to record the titles of up to five relevant articles; and a series of quantitative and qualitative questions regarding ease-of-use, relevancy of results, overall preference (if any between the two resources, likeliness of future use and other preferred research tools. Half of the participants received a worksheet with instructions to search the federated search tool before the single database; the order was reversed for the other half of the students. The evaluation worksheet was designed to be completed in one hour.Participant responses to qualitative questions were analyzed, codified and grouped into thematic categories. If a student mentioned more than one factor in responding to a question, their response was recorded in multiple categories.Main Results

  15. Parallel database search and prime factorization with magnonic holographic memory devices

    Energy Technology Data Exchange (ETDEWEB)

    Khitun, Alexander [Electrical and Computer Engineering Department, University of California - Riverside, Riverside, California 92521 (United States)

    2015-12-28

    In this work, we describe the capabilities of Magnonic Holographic Memory (MHM) for parallel database search and prime factorization. MHM is a type of holographic device, which utilizes spin waves for data transfer and processing. Its operation is based on the correlation between the phases and the amplitudes of the input spin waves and the output inductive voltage. The input of MHM is provided by the phased array of spin wave generating elements allowing the producing of phase patterns of an arbitrary form. The latter makes it possible to code logic states into the phases of propagating waves and exploit wave superposition for parallel data processing. We present the results of numerical modeling illustrating parallel database search and prime factorization. The results of numerical simulations on the database search are in agreement with the available experimental data. The use of classical wave interference may results in a significant speedup over the conventional digital logic circuits in special task data processing (e.g., √n in database search). Potentially, magnonic holographic devices can be implemented as complementary logic units to digital processors. Physical limitations and technological constrains of the spin wave approach are also discussed.

  16. Parallel database search and prime factorization with magnonic holographic memory devices

    Science.gov (United States)

    Khitun, Alexander

    2015-12-01

    In this work, we describe the capabilities of Magnonic Holographic Memory (MHM) for parallel database search and prime factorization. MHM is a type of holographic device, which utilizes spin waves for data transfer and processing. Its operation is based on the correlation between the phases and the amplitudes of the input spin waves and the output inductive voltage. The input of MHM is provided by the phased array of spin wave generating elements allowing the producing of phase patterns of an arbitrary form. The latter makes it possible to code logic states into the phases of propagating waves and exploit wave superposition for parallel data processing. We present the results of numerical modeling illustrating parallel database search and prime factorization. The results of numerical simulations on the database search are in agreement with the available experimental data. The use of classical wave interference may results in a significant speedup over the conventional digital logic circuits in special task data processing (e.g., √n in database search). Potentially, magnonic holographic devices can be implemented as complementary logic units to digital processors. Physical limitations and technological constrains of the spin wave approach are also discussed.

  17. Parallel database search and prime factorization with magnonic holographic memory devices

    International Nuclear Information System (INIS)

    Khitun, Alexander

    2015-01-01

    In this work, we describe the capabilities of Magnonic Holographic Memory (MHM) for parallel database search and prime factorization. MHM is a type of holographic device, which utilizes spin waves for data transfer and processing. Its operation is based on the correlation between the phases and the amplitudes of the input spin waves and the output inductive voltage. The input of MHM is provided by the phased array of spin wave generating elements allowing the producing of phase patterns of an arbitrary form. The latter makes it possible to code logic states into the phases of propagating waves and exploit wave superposition for parallel data processing. We present the results of numerical modeling illustrating parallel database search and prime factorization. The results of numerical simulations on the database search are in agreement with the available experimental data. The use of classical wave interference may results in a significant speedup over the conventional digital logic circuits in special task data processing (e.g., √n in database search). Potentially, magnonic holographic devices can be implemented as complementary logic units to digital processors. Physical limitations and technological constrains of the spin wave approach are also discussed

  18. Searching for evidence or approval? A commentary on database search in systematic reviews and alternative information retrieval methodologies.

    Science.gov (United States)

    Delaney, Aogán; Tamás, Peter A

    2018-03-01

    Despite recognition that database search alone is inadequate even within the health sciences, it appears that reviewers in fields that have adopted systematic review are choosing to rely primarily, or only, on database search for information retrieval. This commentary reminds readers of factors that call into question the appropriateness of default reliance on database searches particularly as systematic review is adapted for use in new and lower consensus fields. It then discusses alternative methods for information retrieval that require development, formalisation, and evaluation. Our goals are to encourage reviewers to reflect critically and transparently on their choice of information retrieval methods and to encourage investment in research on alternatives. Copyright © 2017 John Wiley & Sons, Ltd.

  19. AIDSinfo Drug Database

    Science.gov (United States)

    ... AIDS Drugs Clinical Trials Apps skip to content Drugs Home Drugs Find information on FDA-approved HIV/ ... infection drugs and investigational HIV/AIDS drugs. Search Drugs Search drug Search Icon What's this? Close Popup ...

  20. Chapter 51: How to Build a Simple Cone Search Service Using a Local Database

    Science.gov (United States)

    Kent, B. R.; Greene, G. R.

    The cone search service protocol will be examined from the server side in this chapter. A simple cone search service will be setup and configured locally using MySQL. Data will be read into a table, and the Java JDBC will be used to connect to the database. Readers will understand the VO cone search specification and how to use it to query a database on their local systems and return an XML/VOTable file based on an input of RA/DEC coordinates and a search radius. The cone search in this example will be deployed as a Java servlet. The resulting cone search can be tested with a verification service. This basic setup can be used with other languages and relational databases.

  1. The new ENSDF search system NESSY: IBM/PC nuclear spectroscopy database

    International Nuclear Information System (INIS)

    Boboshin, I.N.; Varlamov, V.V.

    1996-01-01

    The universal relational nuclear structure and decay database NESSY (New ENSDF Search SYstem) developed for the IBM/PC and compatible PCs, and based on the international file ENSDF (Evaluated Nuclear Structure Data File), is described. The NESSY provides the possibility of high efficiency processing (the search and retrieval of any kind of physical data) of the information from ENSDF. The principles of the database development are described and examples of applications are presented. (orig.)

  2. A Taxonomic Search Engine: federating taxonomic databases using web services.

    Science.gov (United States)

    Page, Roderic D M

    2005-03-09

    The taxonomic name of an organism is a key link between different databases that store information on that organism. However, in the absence of a single, comprehensive database of organism names, individual databases lack an easy means of checking the correctness of a name. Furthermore, the same organism may have more than one name, and the same name may apply to more than one organism. The Taxonomic Search Engine (TSE) is a web application written in PHP that queries multiple taxonomic databases (ITIS, Index Fungorum, IPNI, NCBI, and uBIO) and summarises the results in a consistent format. It supports "drill-down" queries to retrieve a specific record. The TSE can optionally suggest alternative spellings the user can try. It also acts as a Life Science Identifier (LSID) authority for the source taxonomic databases, providing globally unique identifiers (and associated metadata) for each name. The Taxonomic Search Engine is available at http://darwin.zoology.gla.ac.uk/~rpage/portal/ and provides a simple demonstration of the potential of the federated approach to providing access to taxonomic names.

  3. STEPS: a grid search methodology for optimized peptide identification filtering of MS/MS database search results.

    Science.gov (United States)

    Piehowski, Paul D; Petyuk, Vladislav A; Sandoval, John D; Burnum, Kristin E; Kiebel, Gary R; Monroe, Matthew E; Anderson, Gordon A; Camp, David G; Smith, Richard D

    2013-03-01

    For bottom-up proteomics, there are wide variety of database-searching algorithms in use for matching peptide sequences to tandem MS spectra. Likewise, there are numerous strategies being employed to produce a confident list of peptide identifications from the different search algorithm outputs. Here we introduce a grid-search approach for determining optimal database filtering criteria in shotgun proteomics data analyses that is easily adaptable to any search. Systematic Trial and Error Parameter Selection--referred to as STEPS--utilizes user-defined parameter ranges to test a wide array of parameter combinations to arrive at an optimal "parameter set" for data filtering, thus maximizing confident identifications. The benefits of this approach in terms of numbers of true-positive identifications are demonstrated using datasets derived from immunoaffinity-depleted blood serum and a bacterial cell lysate, two common proteomics sample types. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Searching for religion and mental health studies required health, social science, and grey literature databases.

    Science.gov (United States)

    Wright, Judy M; Cottrell, David J; Mir, Ghazala

    2014-07-01

    To determine the optimal databases to search for studies of faith-sensitive interventions for treating depression. We examined 23 health, social science, religious, and grey literature databases searched for an evidence synthesis. Databases were prioritized by yield of (1) search results, (2) potentially relevant references identified during screening, (3) included references contained in the synthesis, and (4) included references that were available in the database. We assessed the impact of databases beyond MEDLINE, EMBASE, and PsycINFO by their ability to supply studies identifying new themes and issues. We identified pragmatic workload factors that influence database selection. PsycINFO was the best performing database within all priority lists. ArabPsyNet, CINAHL, Dissertations and Theses, EMBASE, Global Health, Health Management Information Consortium, MEDLINE, PsycINFO, and Sociological Abstracts were essential for our searches to retrieve the included references. Citation tracking activities and the personal library of one of the research teams made significant contributions of unique, relevant references. Religion studies databases (Am Theo Lib Assoc, FRANCIS) did not provide unique, relevant references. Literature searches for reviews and evidence syntheses of religion and health studies should include social science, grey literature, non-Western databases, personal libraries, and citation tracking activities. Copyright © 2014 Elsevier Inc. All rights reserved.

  5. Hypnotic Medications and Suicide: Risk, Mechanisms, Mitigation, and the FDA.

    Science.gov (United States)

    McCall, W Vaughn; Benca, Ruth M; Rosenquist, Peter B; Riley, Mary Anne; McCloud, Laryssa; Newman, Jill C; Case, Doug; Rumble, Meredith; Krystal, Andrew D

    2017-01-01

    Insomnia is associated with increased risk for suicide. The Food and Drug Administration (FDA) has mandated that warnings regarding suicide be included in the prescribing information for hypnotic medications. The authors conducted a review of the evidence for and against the claim that hypnotics increase the risk of suicide. This review focused on modern, FDA-approved hypnotics, beginning with the introduction of benzodiazepines, limiting its findings to adults. PubMed and Web of Science were searched, crossing the terms "suicide" and "suicidal" with each of the modern FDA-approved hypnotics. The FDA web site was searched for postmarketing safety reviews, and the FDA was contacted with requests to provide detailed case reports for hypnotic-related suicide deaths reported through its Adverse Event Reporting System. Epidemiological studies show that hypnotics are associated with an increased risk for suicide. However, none of these studies adequately controlled for depression or other psychiatric disorders that may be linked with insomnia. Suicide deaths have been reported from single-agent hypnotic overdoses. A separate concern is that benzodiazepine receptor agonist hypnotics can cause parasomnias, which in rare cases may lead to suicidal ideation or suicidal behavior in persons who were not known to be suicidal. On the other hand, ongoing research is testing whether treatment of insomnia may reduce suicidality in adults with depression. The review findings indicate that hypnotic medications are associated with suicidal ideation. Future studies should be designed to assess whether increases in suicidality result from CNS impairments from a given hypnotic medication or whether such medication decreases suicidality because of improvements in insomnia.

  6. PIR search result - KOME | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available e filtered with Expect values lower than 1e-10. Number of data entries 1,549,409 ...he searches. Data analysis method Performed blastx searches against the PIR protein database. The results ar

  7. A Taxonomic Search Engine: Federating taxonomic databases using web services

    Directory of Open Access Journals (Sweden)

    Page Roderic DM

    2005-03-01

    Full Text Available Abstract Background The taxonomic name of an organism is a key link between different databases that store information on that organism. However, in the absence of a single, comprehensive database of organism names, individual databases lack an easy means of checking the correctness of a name. Furthermore, the same organism may have more than one name, and the same name may apply to more than one organism. Results The Taxonomic Search Engine (TSE is a web application written in PHP that queries multiple taxonomic databases (ITIS, Index Fungorum, IPNI, NCBI, and uBIO and summarises the results in a consistent format. It supports "drill-down" queries to retrieve a specific record. The TSE can optionally suggest alternative spellings the user can try. It also acts as a Life Science Identifier (LSID authority for the source taxonomic databases, providing globally unique identifiers (and associated metadata for each name. Conclusion The Taxonomic Search Engine is available at http://darwin.zoology.gla.ac.uk/~rpage/portal/ and provides a simple demonstration of the potential of the federated approach to providing access to taxonomic names.

  8. pSort search result - KOME | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...name: kome_psort_search_result.zip File URL: ftp://ftp.biosciencedbc.jp/archive/kome/LATEST/kome_psort_searc...abase Description Download License Update History of This Database Site Policy | Contact Us pSort search result - KOME | LSDB Archive ...

  9. PFTijah: text search in an XML database system

    NARCIS (Netherlands)

    Hiemstra, Djoerd; Rode, H.; van Os, R.; Flokstra, Jan

    2006-01-01

    This paper introduces the PFTijah system, a text search system that is integrated with an XML/XQuery database management system. We present examples of its use, we explain some of the system internals, and discuss plans for future work. PFTijah is part of the open source release of MonetDB/XQuery.

  10. A Bayesian network approach to the database search problem in criminal proceedings

    Science.gov (United States)

    2012-01-01

    Background The ‘database search problem’, that is, the strengthening of a case - in terms of probative value - against an individual who is found as a result of a database search, has been approached during the last two decades with substantial mathematical analyses, accompanied by lively debate and centrally opposing conclusions. This represents a challenging obstacle in teaching but also hinders a balanced and coherent discussion of the topic within the wider scientific and legal community. This paper revisits and tracks the associated mathematical analyses in terms of Bayesian networks. Their derivation and discussion for capturing probabilistic arguments that explain the database search problem are outlined in detail. The resulting Bayesian networks offer a distinct view on the main debated issues, along with further clarity. Methods As a general framework for representing and analyzing formal arguments in probabilistic reasoning about uncertain target propositions (that is, whether or not a given individual is the source of a crime stain), this paper relies on graphical probability models, in particular, Bayesian networks. This graphical probability modeling approach is used to capture, within a single model, a series of key variables, such as the number of individuals in a database, the size of the population of potential crime stain sources, and the rarity of the corresponding analytical characteristics in a relevant population. Results This paper demonstrates the feasibility of deriving Bayesian network structures for analyzing, representing, and tracking the database search problem. The output of the proposed models can be shown to agree with existing but exclusively formulaic approaches. Conclusions The proposed Bayesian networks allow one to capture and analyze the currently most well-supported but reputedly counter-intuitive and difficult solution to the database search problem in a way that goes beyond the traditional, purely formulaic expressions

  11. Combined semantic and similarity search in medical image databases

    Science.gov (United States)

    Seifert, Sascha; Thoma, Marisa; Stegmaier, Florian; Hammon, Matthias; Kramer, Martin; Huber, Martin; Kriegel, Hans-Peter; Cavallaro, Alexander; Comaniciu, Dorin

    2011-03-01

    The current diagnostic process at hospitals is mainly based on reviewing and comparing images coming from multiple time points and modalities in order to monitor disease progression over a period of time. However, for ambiguous cases the radiologist deeply relies on reference literature or second opinion. Although there is a vast amount of acquired images stored in PACS systems which could be reused for decision support, these data sets suffer from weak search capabilities. Thus, we present a search methodology which enables the physician to fulfill intelligent search scenarios on medical image databases combining ontology-based semantic and appearance-based similarity search. It enabled the elimination of 12% of the top ten hits which would arise without taking the semantic context into account.

  12. Efficiency of Database Search for Identification of Mutated and Modified Proteins via Mass Spectrometry

    OpenAIRE

    Pevzner, Pavel A.; Mulyukov, Zufar; Dancik, Vlado; Tang, Chris L

    2001-01-01

    Although protein identification by matching tandem mass spectra (MS/MS) against protein databases is a widespread tool in mass spectrometry, the question about reliability of such searches remains open. Absence of rigorous significance scores in MS/MS database search makes it difficult to discard random database hits and may lead to erroneous protein identification, particularly in the case of mutated or post-translationally modified peptides. This problem is especially important for high-thr...

  13. Winnowing sequences from a database search.

    Science.gov (United States)

    Berman, P; Zhang, Z; Wolf, Y I; Koonin, E V; Miller, W

    2000-01-01

    In database searches for sequence similarity, matches to a distinct sequence region (e.g., protein domain) are frequently obscured by numerous matches to another region of the same sequence. In order to cope with this problem, algorithms are developed to discard redundant matches. One model for this problem begins with a list of intervals, each with an associated score; each interval gives the range of positions in the query sequence that align to a database sequence, and the score is that of the alignment. If interval I is contained in interval J, and I's score is less than J's, then I is said to be dominated by J. The problem is then to identify each interval that is dominated by at least K other intervals, where K is a given level of "tolerable redundancy." An algorithm is developed to solve the problem in O(N log N) time and O(N*) space, where N is the number of intervals and N* is a precisely defined value that never exceeds N and is frequently much smaller. This criterion for discarding database hits has been implemented in the Blast program, as illustrated herein with examples. Several variations and extensions of this approach are also described.

  14. The database search problem: a question of rational decision making.

    Science.gov (United States)

    Gittelson, S; Biedermann, A; Bozza, S; Taroni, F

    2012-10-10

    This paper applies probability and decision theory in the graphical interface of an influence diagram to study the formal requirements of rationality which justify the individualization of a person found through a database search. The decision-theoretic part of the analysis studies the parameters that a rational decision maker would use to individualize the selected person. The modeling part (in the form of an influence diagram) clarifies the relationships between this decision and the ingredients that make up the database search problem, i.e., the results of the database search and the different pairs of propositions describing whether an individual is at the source of the crime stain. These analyses evaluate the desirability associated with the decision of 'individualizing' (and 'not individualizing'). They point out that this decision is a function of (i) the probability that the individual in question is, in fact, at the source of the crime stain (i.e., the state of nature), and (ii) the decision maker's preferences among the possible consequences of the decision (i.e., the decision maker's loss function). We discuss the relevance and argumentative implications of these insights with respect to recent comments in specialized literature, which suggest points of view that are opposed to the results of our study. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  15. The LAILAPS search engine: a feature model for relevance ranking in life science databases.

    Science.gov (United States)

    Lange, Matthias; Spies, Karl; Colmsee, Christian; Flemming, Steffen; Klapperstück, Matthias; Scholz, Uwe

    2010-03-25

    Efficient and effective information retrieval in life sciences is one of the most pressing challenge in bioinformatics. The incredible growth of life science databases to a vast network of interconnected information systems is to the same extent a big challenge and a great chance for life science research. The knowledge found in the Web, in particular in life-science databases, are a valuable major resource. In order to bring it to the scientist desktop, it is essential to have well performing search engines. Thereby, not the response time nor the number of results is important. The most crucial factor for millions of query results is the relevance ranking. In this paper, we present a feature model for relevance ranking in life science databases and its implementation in the LAILAPS search engine. Motivated by the observation of user behavior during their inspection of search engine result, we condensed a set of 9 relevance discriminating features. These features are intuitively used by scientists, who briefly screen database entries for potential relevance. The features are both sufficient to estimate the potential relevance, and efficiently quantifiable. The derivation of a relevance prediction function that computes the relevance from this features constitutes a regression problem. To solve this problem, we used artificial neural networks that have been trained with a reference set of relevant database entries for 19 protein queries. Supporting a flexible text index and a simple data import format, this concepts are implemented in the LAILAPS search engine. It can easily be used both as search engine for comprehensive integrated life science databases and for small in-house project databases. LAILAPS is publicly available for SWISSPROT data at http://lailaps.ipk-gatersleben.de.

  16. Global search tool for the Advanced Photon Source Integrated Relational Model of Installed Systems (IRMIS) database

    International Nuclear Information System (INIS)

    Quock, D.E.R.; Cianciarulo, M.B.

    2007-01-01

    The Integrated Relational Model of Installed Systems (IRMIS) is a relational database tool that has been implemented at the Advanced Photon Source to maintain an updated account of approximately 600 control system software applications, 400,000 process variables, and 30,000 control system hardware components. To effectively display this large amount of control system information to operators and engineers, IRMIS was initially built with nine Web-based viewers: Applications Organizing Index, IOC, PLC, Component Type, Installed Components, Network, Controls Spares, Process Variables, and Cables. However, since each viewer is designed to provide details from only one major category of the control system, the necessity for a one-stop global search tool for the entire database became apparent. The user requirements for extremely fast database search time and ease of navigation through search results led to the choice of Asynchronous JavaScript and XML (AJAX) technology in the implementation of the IRMIS global search tool. Unique features of the global search tool include a two-tier level of displayed search results, and a database data integrity validation and reporting mechanism.

  17. mirPub: a database for searching microRNA publications.

    Science.gov (United States)

    Vergoulis, Thanasis; Kanellos, Ilias; Kostoulas, Nikos; Georgakilas, Georgios; Sellis, Timos; Hatzigeorgiou, Artemis; Dalamagas, Theodore

    2015-05-01

    Identifying, amongst millions of publications available in MEDLINE, those that are relevant to specific microRNAs (miRNAs) of interest based on keyword search faces major obstacles. References to miRNA names in the literature often deviate from standard nomenclature for various reasons, since even the official nomenclature evolves. For instance, a single miRNA name may identify two completely different molecules or two different names may refer to the same molecule. mirPub is a database with a powerful and intuitive interface, which facilitates searching for miRNA literature, addressing the aforementioned issues. To provide effective search services, mirPub applies text mining techniques on MEDLINE, integrates data from several curated databases and exploits data from its user community following a crowdsourcing approach. Other key features include an interactive visualization service that illustrates intuitively the evolution of miRNA data, tag clouds summarizing the relevance of publications to particular diseases, cell types or tissues and access to TarBase 6.0 data to oversee genes related to miRNA publications. mirPub is freely available at http://www.microrna.gr/mirpub/. vergoulis@imis.athena-innovation.gr or dalamag@imis.athena-innovation.gr Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

  18. What is lost when searching only one literature database for articles relevant to injury prevention and safety promotion?

    Science.gov (United States)

    Lawrence, D W

    2008-12-01

    To assess what is lost if only one literature database is searched for articles relevant to injury prevention and safety promotion (IPSP) topics. Serial textword (keyword, free-text) searches using multiple synonym terms for five key IPSP topics (bicycle-related brain injuries, ethanol-impaired driving, house fires, road rage, and suicidal behaviors among adolescents) were conducted in four of the bibliographic databases that are most used by IPSP professionals: EMBASE, MEDLINE, PsycINFO, and Web of Science. Through a systematic procedure, an inventory of articles on each topic in each database was conducted to identify the total unduplicated count of all articles on each topic, the number of articles unique to each database, and the articles available if only one database is searched. No single database included all of the relevant articles on any topic, and the database with the broadest coverage differed by topic. A search of only one literature database will return 16.7-81.5% (median 43.4%) of the available articles on any of five key IPSP topics. Each database contributed unique articles to the total bibliography for each topic. A literature search performed in only one database will, on average, lead to a loss of more than half of the available literature on a topic.

  19. New FDA-Approved Disease-Modifying Therapies for Multiple Sclerosis.

    Science.gov (United States)

    English, Clayton; Aloi, Joseph J

    2015-04-01

    Interferon injectables and glatiramer acetate have served as the primary disease-modifying treatments for multiple sclerosis (MS) since their introduction in the 1990s and are first-line treatments for relapsing-remitting forms of MS (RRMS). Many new drug therapies were launched since early 2010, expanding the drug treatment options considerably in a disease state that once had a limited treatment portfolio. The purpose of this review is to critically evaluate the safety profile and efficacy data of disease-modifying agents for MS approved by the US Food and Drug Administration (FDA) from 2010 to the present and provide cost and available pharmacoeconomic data about each new treatment. Peer-reviewed clinical trials, pharmacoeconomic studies, and relevant pharmacokinetic/pharmacologic studies were identified from MEDLINE (January 2000-December 2014) by using the search terms multiple sclerosis, fingolimod, teriflunomide, alemtuzumab, dimethyl fumarate, pegylated interferon, peginterferon beta-1a, glatiramer 3 times weekly, and pharmacoeconomics. Citations from available articles were also reviewed for additional references. The databases publically available at www.clinicaltrials.gov and www.fda.gov were searched for unpublished studies or studies currently in progress. A total of 5 new agents and 1 new dosage formulation were approved by the FDA for the treatment of RRMS since 2010. Peginterferon beta-1a and high-dose glatiramer acetate represent 2 new effective injectable options for MS that reduce burden of administration seen with traditional interferon and low-dose glatiramer acetate. Fingolimod, teriflunomide, and dimethyl fumarate represent new oral agents available for MS, and their efficacy in reducing annualized relapse rates is 48% to 55%, 22% to 36.3%, and 44% to 53%, respectively, compared with placebo. Alemtuzumab is a biologic given over a 2-year span that reduced annualized relapse rates by 55% in treatment-naive patients and by 49% in patients

  20. Enriching Great Britain's National Landslide Database by searching newspaper archives

    Science.gov (United States)

    Taylor, Faith E.; Malamud, Bruce D.; Freeborough, Katy; Demeritt, David

    2015-11-01

    Our understanding of where landslide hazard and impact will be greatest is largely based on our knowledge of past events. Here, we present a method to supplement existing records of landslides in Great Britain by searching an electronic archive of regional newspapers. In Great Britain, the British Geological Survey (BGS) is responsible for updating and maintaining records of landslide events and their impacts in the National Landslide Database (NLD). The NLD contains records of more than 16,500 landslide events in Great Britain. Data sources for the NLD include field surveys, academic articles, grey literature, news, public reports and, since 2012, social media. We aim to supplement the richness of the NLD by (i) identifying additional landslide events, (ii) acting as an additional source of confirmation of events existing in the NLD and (iii) adding more detail to existing database entries. This is done by systematically searching the Nexis UK digital archive of 568 regional newspapers published in the UK. In this paper, we construct a robust Boolean search criterion by experimenting with landslide terminology for four training periods. We then apply this search to all articles published in 2006 and 2012. This resulted in the addition of 111 records of landslide events to the NLD over the 2 years investigated (2006 and 2012). We also find that we were able to obtain information about landslide impact for 60-90% of landslide events identified from newspaper articles. Spatial and temporal patterns of additional landslides identified from newspaper articles are broadly in line with those existing in the NLD, confirming that the NLD is a representative sample of landsliding in Great Britain. This method could now be applied to more time periods and/or other hazards to add richness to databases and thus improve our ability to forecast future events based on records of past events.

  1. Anatomy and evolution of database search engines-a central component of mass spectrometry based proteomic workflows.

    Science.gov (United States)

    Verheggen, Kenneth; Raeder, Helge; Berven, Frode S; Martens, Lennart; Barsnes, Harald; Vaudel, Marc

    2017-09-13

    Sequence database search engines are bioinformatics algorithms that identify peptides from tandem mass spectra using a reference protein sequence database. Two decades of development, notably driven by advances in mass spectrometry, have provided scientists with more than 30 published search engines, each with its own properties. In this review, we present the common paradigm behind the different implementations, and its limitations for modern mass spectrometry datasets. We also detail how the search engines attempt to alleviate these limitations, and provide an overview of the different software frameworks available to the researcher. Finally, we highlight alternative approaches for the identification of proteomic mass spectrometry datasets, either as a replacement for, or as a complement to, sequence database search engines. © 2017 Wiley Periodicals, Inc.

  2. Security and privacy qualities of medical devices: an analysis of FDA postmarket surveillance.

    Science.gov (United States)

    Kramer, Daniel B; Baker, Matthew; Ransford, Benjamin; Molina-Markham, Andres; Stewart, Quinn; Fu, Kevin; Reynolds, Matthew R

    2012-01-01

    Medical devices increasingly depend on computing functions such as wireless communication and Internet connectivity for software-based control of therapies and network-based transmission of patients' stored medical information. These computing capabilities introduce security and privacy risks, yet little is known about the prevalence of such risks within the clinical setting. We used three comprehensive, publicly available databases maintained by the Food and Drug Administration (FDA) to evaluate recalls and adverse events related to security and privacy risks of medical devices. Review of weekly enforcement reports identified 1,845 recalls; 605 (32.8%) of these included computers, 35 (1.9%) stored patient data, and 31 (1.7%) were capable of wireless communication. Searches of databases specific to recalls and adverse events identified only one event with a specific connection to security or privacy. Software-related recalls were relatively common, and most (81.8%) mentioned the possibility of upgrades, though only half of these provided specific instructions for the update mechanism. Our review of recalls and adverse events from federal government databases reveals sharp inconsistencies with databases at individual providers with respect to security and privacy risks. Recalls related to software may increase security risks because of unprotected update and correction mechanisms. To detect signals of security and privacy problems that adversely affect public health, federal postmarket surveillance strategies should rethink how to effectively and efficiently collect data on security and privacy problems in devices that increasingly depend on computing systems susceptible to malware.

  3. Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation.

    Science.gov (United States)

    Rognes, Torbjørn

    2011-06-01

    The Smith-Waterman algorithm for local sequence alignment is more sensitive than heuristic methods for database searching, but also more time-consuming. The fastest approach to parallelisation with SIMD technology has previously been described by Farrar in 2007. The aim of this study was to explore whether further speed could be gained by other approaches to parallelisation. A faster approach and implementation is described and benchmarked. In the new tool SWIPE, residues from sixteen different database sequences are compared in parallel to one query residue. Using a 375 residue query sequence a speed of 106 billion cell updates per second (GCUPS) was achieved on a dual Intel Xeon X5650 six-core processor system, which is over six times more rapid than software based on Farrar's 'striped' approach. SWIPE was about 2.5 times faster when the programs used only a single thread. For shorter queries, the increase in speed was larger. SWIPE was about twice as fast as BLAST when using the BLOSUM50 score matrix, while BLAST was about twice as fast as SWIPE for the BLOSUM62 matrix. The software is designed for 64 bit Linux on processors with SSSE3. Source code is available from http://dna.uio.no/swipe/ under the GNU Affero General Public License. Efficient parallelisation using SIMD on standard hardware makes it possible to run Smith-Waterman database searches more than six times faster than before. The approach described here could significantly widen the potential application of Smith-Waterman searches. Other applications that require optimal local alignment scores could also benefit from improved performance.

  4. Indexing Bibliographic Database Content Using MariaDB and Sphinx Search Server

    Directory of Open Access Journals (Sweden)

    Arie Nugraha

    2014-07-01

    Full Text Available Fast retrieval of digital content has become mandatory for library and archive information systems. Many software applications have emerged to handle the indexing of digital content, from low-level ones such Apache Lucene, to more RESTful and web-services-ready ones such Apache Solr and ElasticSearch. Solr’s popularity among library software developers makes it the “de-facto” standard software for indexing digital content. For content (full-text content or bibliographic description already stored inside a relational DBMS such as MariaDB (a fork of MySQL or PostgreSQL, Sphinx Search Server (Sphinx is a suitable alternative. This article will cover an introduction on how to use Sphinx with MariaDB databases to index database content as well as some examples of Sphinx API usage.

  5. Agreements and Discrepancies between FDA Reports and Journal Papers on Biologic Agents Approved for Rheumatoid Arthritis

    DEFF Research Database (Denmark)

    Amarilyo, Gil; Furst, Daniel E; Woo, Jennifer M P

    2016-01-01

    BACKGROUND: Sponsors that seek to commercialize new drugs apply to the Food and Drug Administration (FDA) which independently analyzes the raw data and reports the results on its website. OBJECTIVES: This study sought to determine if there are differences between the FDA assessments and journal...... reports on biologic agents developed for the treatment of rheumatoid arthritis. METHODS: Available data on FDA-approved drugs were extracted from the website, and a systematic literature search was conducted to identify matching studies in peer-reviewed medical journals. Outcome measures were the American...... College of Rheumatology response criteria ACR20 (efficacy) and withdrawal due to adverse events (safety). As effect size odds ratios were estimated for each active trial arm vs. control arm (i.e. for both sources: FDA and journal report), followed by calculation of the ratios of the FDA and journal report...

  6. Metagenomic Taxonomy-Guided Database-Searching Strategy for Improving Metaproteomic Analysis.

    Science.gov (United States)

    Xiao, Jinqiu; Tanca, Alessandro; Jia, Ben; Yang, Runqing; Wang, Bo; Zhang, Yu; Li, Jing

    2018-04-06

    Metaproteomics provides a direct measure of the functional information by investigating all proteins expressed by a microbiota. However, due to the complexity and heterogeneity of microbial communities, it is very hard to construct a sequence database suitable for a metaproteomic study. Using a public database, researchers might not be able to identify proteins from poorly characterized microbial species, while a sequencing-based metagenomic database may not provide adequate coverage for all potentially expressed protein sequences. To address this challenge, we propose a metagenomic taxonomy-guided database-search strategy (MT), in which a merged database is employed, consisting of both taxonomy-guided reference protein sequences from public databases and proteins from metagenome assembly. By applying our MT strategy to a mock microbial mixture, about two times as many peptides were detected as with the metagenomic database only. According to the evaluation of the reliability of taxonomic attribution, the rate of misassignments was comparable to that obtained using an a priori matched database. We also evaluated the MT strategy with a human gut microbial sample, and we found 1.7 times as many peptides as using a standard metagenomic database. In conclusion, our MT strategy allows the construction of databases able to provide high sensitivity and precision in peptide identification in metaproteomic studies, enabling the detection of proteins from poorly characterized species within the microbiota.

  7. IMPROVED SEARCH OF PRINCIPAL COMPONENT ANALYSIS DATABASES FOR SPECTRO-POLARIMETRIC INVERSION

    International Nuclear Information System (INIS)

    Casini, R.; Lites, B. W.; Ramos, A. Asensio; Ariste, A. López

    2013-01-01

    We describe a simple technique for the acceleration of spectro-polarimetric inversions based on principal component analysis (PCA) of Stokes profiles. This technique involves the indexing of the database models based on the sign of the projections (PCA coefficients) of the first few relevant orders of principal components of the four Stokes parameters. In this way, each model in the database can be attributed a distinctive binary number of 2 4n bits, where n is the number of PCA orders used for the indexing. Each of these binary numbers (indices) identifies a group of ''compatible'' models for the inversion of a given set of observed Stokes profiles sharing the same index. The complete set of the binary numbers so constructed evidently determines a partition of the database. The search of the database for the PCA inversion of spectro-polarimetric data can profit greatly from this indexing. In practical cases it becomes possible to approach the ideal acceleration factor of 2 4n as compared to the systematic search of a non-indexed database for a traditional PCA inversion. This indexing method relies on the existence of a physical meaning in the sign of the PCA coefficients of a model. For this reason, the presence of model ambiguities and of spectro-polarimetric noise in the observations limits in practice the number n of relevant PCA orders that can be used for the indexing

  8. Dissolution Methods Database

    Data.gov (United States)

    U.S. Department of Health & Human Services — For a drug product that does not have a dissolution test method in the United States Pharmacopeia (USP), the FDA Dissolution Methods Database provides information on...

  9. Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation

    Directory of Open Access Journals (Sweden)

    Rognes Torbjørn

    2011-06-01

    Full Text Available Abstract Background The Smith-Waterman algorithm for local sequence alignment is more sensitive than heuristic methods for database searching, but also more time-consuming. The fastest approach to parallelisation with SIMD technology has previously been described by Farrar in 2007. The aim of this study was to explore whether further speed could be gained by other approaches to parallelisation. Results A faster approach and implementation is described and benchmarked. In the new tool SWIPE, residues from sixteen different database sequences are compared in parallel to one query residue. Using a 375 residue query sequence a speed of 106 billion cell updates per second (GCUPS was achieved on a dual Intel Xeon X5650 six-core processor system, which is over six times more rapid than software based on Farrar's 'striped' approach. SWIPE was about 2.5 times faster when the programs used only a single thread. For shorter queries, the increase in speed was larger. SWIPE was about twice as fast as BLAST when using the BLOSUM50 score matrix, while BLAST was about twice as fast as SWIPE for the BLOSUM62 matrix. The software is designed for 64 bit Linux on processors with SSSE3. Source code is available from http://dna.uio.no/swipe/ under the GNU Affero General Public License. Conclusions Efficient parallelisation using SIMD on standard hardware makes it possible to run Smith-Waterman database searches more than six times faster than before. The approach described here could significantly widen the potential application of Smith-Waterman searches. Other applications that require optimal local alignment scores could also benefit from improved performance.

  10. Term Relevance Feedback and Mediated Database Searching: Implications for Information Retrieval Practice and Systems Design.

    Science.gov (United States)

    Spink, Amanda

    1995-01-01

    This study uses the human approach to examine the sources and effectiveness of search terms selected during 40 mediated interactive database searches and focuses on determining the retrieval effectiveness of search terms identified by users and intermediaries from retrieved items during term relevance feedback. (Author/JKP)

  11. DOT Online Database

    Science.gov (United States)

    Page Home Table of Contents Contents Search Database Search Login Login Databases Advisory Circulars accessed by clicking below: Full-Text WebSearch Databases Database Records Date Advisory Circulars 2092 5 data collection and distribution policies. Document Database Website provided by MicroSearch

  12. Security and Privacy Qualities of Medical Devices: An Analysis of FDA Postmarket Surveillance

    Science.gov (United States)

    Kramer, Daniel B.; Baker, Matthew; Ransford, Benjamin; Molina-Markham, Andres; Stewart, Quinn; Fu, Kevin; Reynolds, Matthew R.

    2012-01-01

    Background Medical devices increasingly depend on computing functions such as wireless communication and Internet connectivity for software-based control of therapies and network-based transmission of patients’ stored medical information. These computing capabilities introduce security and privacy risks, yet little is known about the prevalence of such risks within the clinical setting. Methods We used three comprehensive, publicly available databases maintained by the Food and Drug Administration (FDA) to evaluate recalls and adverse events related to security and privacy risks of medical devices. Results Review of weekly enforcement reports identified 1,845 recalls; 605 (32.8%) of these included computers, 35 (1.9%) stored patient data, and 31 (1.7%) were capable of wireless communication. Searches of databases specific to recalls and adverse events identified only one event with a specific connection to security or privacy. Software-related recalls were relatively common, and most (81.8%) mentioned the possibility of upgrades, though only half of these provided specific instructions for the update mechanism. Conclusions Our review of recalls and adverse events from federal government databases reveals sharp inconsistencies with databases at individual providers with respect to security and privacy risks. Recalls related to software may increase security risks because of unprotected update and correction mechanisms. To detect signals of security and privacy problems that adversely affect public health, federal postmarket surveillance strategies should rethink how to effectively and efficiently collect data on security and privacy problems in devices that increasingly depend on computing systems susceptible to malware. PMID:22829874

  13. FDA regulation of tobacco: blessing or curse for FDA professionals?

    Science.gov (United States)

    O'Reilly, James T

    2009-01-01

    Upwards of 400,000 Americans will die that year from the effects of cigarettes, which FDA will now "regulate" very gently, with its hands tied by a slick statutory protection for the largest existing tobacco marketers. Career FDA professionals will be criticized as enablers of mega-marketers' continued sales, working at the margins, arranging the paperwork for protection of megafirms' market share, and sitting by as the deaths and addictive behaviors continue. "Join the Public Health Service, inspired by a public health mission," they were told, and yet they will be unable to do much regulating of the addictive and fatal products for which they now have titular responsibility. This essay observes that these fine FDA professionals are handed the sticky remains of a messy bargain, negotiated in a distracted Congress by expensive lawyers with clients who were potent contributors to political action committees. The only formula that is not secret about the 2009 law is the way in which industry purchased sufficient allegiance to gather the votes for its adoption. The remaining mystery is how FDA could be expected to do these tasks without losing its best and brightest professionals to other fields.

  14. Supporting ontology-based keyword search over medical databases.

    Science.gov (United States)

    Kementsietsidis, Anastasios; Lim, Lipyeow; Wang, Min

    2008-11-06

    The proliferation of medical terms poses a number of challenges in the sharing of medical information among different stakeholders. Ontologies are commonly used to establish relationships between different terms, yet their role in querying has not been investigated in detail. In this paper, we study the problem of supporting ontology-based keyword search queries on a database of electronic medical records. We present several approaches to support this type of queries, study the advantages and limitations of each approach, and summarize the lessons learned as best practices.

  15. Search extension transforms Wiki into a relational system: a case for flavonoid metabolite database.

    Science.gov (United States)

    Arita, Masanori; Suwa, Kazuhiro

    2008-09-17

    In computer science, database systems are based on the relational model founded by Edgar Codd in 1970. On the other hand, in the area of biology the word 'database' often refers to loosely formatted, very large text files. Although such bio-databases may describe conflicts or ambiguities (e.g. a protein pair do and do not interact, or unknown parameters) in a positive sense, the flexibility of the data format sacrifices a systematic query mechanism equivalent to the widely used SQL. To overcome this disadvantage, we propose embeddable string-search commands on a Wiki-based system and designed a half-formatted database. As proof of principle, a database of flavonoid with 6902 molecular structures from over 1687 plant species was implemented on MediaWiki, the background system of Wikipedia. Registered users can describe any information in an arbitrary format. Structured part is subject to text-string searches to realize relational operations. The system was written in PHP language as the extension of MediaWiki. All modifications are open-source and publicly available. This scheme benefits from both the free-formatted Wiki style and the concise and structured relational-database style. MediaWiki supports multi-user environments for document management, and the cost for database maintenance is alleviated.

  16. Accelerating Smith-Waterman Algorithm for Biological Database Search on CUDA-Compatible GPUs

    Science.gov (United States)

    Munekawa, Yuma; Ino, Fumihiko; Hagihara, Kenichi

    This paper presents a fast method capable of accelerating the Smith-Waterman algorithm for biological database search on a cluster of graphics processing units (GPUs). Our method is implemented using compute unified device architecture (CUDA), which is available on the nVIDIA GPU. As compared with previous methods, our method has four major contributions. (1) The method efficiently uses on-chip shared memory to reduce the data amount being transferred between off-chip video memory and processing elements in the GPU. (2) It also reduces the number of data fetches by applying a data reuse technique to query and database sequences. (3) A pipelined method is also implemented to overlap GPU execution with database access. (4) Finally, a master/worker paradigm is employed to accelerate hundreds of database searches on a cluster system. In experiments, the peak performance on a GeForce GTX 280 card reaches 8.32 giga cell updates per second (GCUPS). We also find that our method reduces the amount of data fetches to 1/140, achieving approximately three times higher performance than a previous CUDA-based method. Our 32-node cluster version is approximately 28 times faster than a single GPU version. Furthermore, the effective performance reaches 75.6 giga instructions per second (GIPS) using 32 GeForce 8800 GTX cards.

  17. CUDASW++: optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units

    Directory of Open Access Journals (Sweden)

    Maskell Douglas L

    2009-05-01

    Full Text Available Abstract Background The Smith-Waterman algorithm is one of the most widely used tools for searching biological sequence databases due to its high sensitivity. Unfortunately, the Smith-Waterman algorithm is computationally demanding, which is further compounded by the exponential growth of sequence databases. The recent emergence of many-core architectures, and their associated programming interfaces, provides an opportunity to accelerate sequence database searches using commonly available and inexpensive hardware. Findings Our CUDASW++ implementation (benchmarked on a single-GPU NVIDIA GeForce GTX 280 graphics card and a dual-GPU GeForce GTX 295 graphics card provides a significant performance improvement compared to other publicly available implementations, such as SWPS3, CBESW, SW-CUDA, and NCBI-BLAST. CUDASW++ supports query sequences of length up to 59K and for query sequences ranging in length from 144 to 5,478 in Swiss-Prot release 56.6, the single-GPU version achieves an average performance of 9.509 GCUPS with a lowest performance of 9.039 GCUPS and a highest performance of 9.660 GCUPS, and the dual-GPU version achieves an average performance of 14.484 GCUPS with a lowest performance of 10.660 GCUPS and a highest performance of 16.087 GCUPS. Conclusion CUDASW++ is publicly available open-source software. It provides a significant performance improvement for Smith-Waterman-based protein sequence database searches by fully exploiting the compute capability of commonly used CUDA-enabled low-cost GPUs.

  18. 77 FR 14404 - Guidance for the Public, Food and Drug Administration (FDA) Advisory Committee Members, and FDA...

    Science.gov (United States)

    2012-03-09

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES Food and Drug Administration [Docket No. FDA-2002-D-0094; (formerly Docket No. 02D-0049)] Guidance for the Public, Food and Drug Administration (FDA) Advisory... Food and Drug Administration (FDA) is announcing the availability of a guidance for the public, FDA...

  19. Current Comparative Table (CCT) automates customized searches of dynamic biological databases.

    Science.gov (United States)

    Landsteiner, Benjamin R; Olson, Michael R; Rutherford, Robert

    2005-07-01

    The Current Comparative Table (CCT) software program enables working biologists to automate customized bioinformatics searches, typically of remote sequence or HMM (hidden Markov model) databases. CCT currently supports BLAST, hmmpfam and other programs useful for gene and ortholog identification. The software is web based, has a BioPerl core and can be used remotely via a browser or locally on Mac OS X or Linux machines. CCT is particularly useful to scientists who study large sets of molecules in today's evolving information landscape because it color-codes all result files by age and highlights even tiny changes in sequence or annotation. By empowering non-bioinformaticians to automate custom searches and examine current results in context at a glance, CCT allows a remote database submission in the evening to influence the next morning's bench experiment. A demonstration of CCT is available at http://orb.public.stolaf.edu/CCTdemo and the open source software is freely available from http://sourceforge.net/projects/orb-cct.

  20. Google Scholar Out-Performs Many Subscription Databases when Keyword Searching. A Review of: Walters, W. H. (2009. Google Scholar search performance: Comparative recall and precision. portal: Libraries and the Academy, 9(1, 5-24.

    Directory of Open Access Journals (Sweden)

    Giovanna Badia

    2010-09-01

    Full Text Available Objective – To compare the search performance (i.e., recall and precision of Google Scholar with that of 11 other bibliographic databases when using a keyword search to find references on later-life migration. Design – Comparative database evaluation. Setting – Not stated in the article. It appears from the author’s affiliation that this research took place in an academic institution of higher learning. Subjects – Twelve databases were compared: Google Scholar, Academic Search Elite, AgeLine, ArticleFirst, EconLit, Geobase, Medline, PAIS International, Popline, Social Sciences Abstracts, Social Sciences Citation Index, and SocIndex. Methods – The relevant literature on later-life migration was pre-identified as a set of 155 journal articles published from 1990 to 2000. The author selected these articles from database searches, citation tracking, journal scans, and consultations with social sciences colleagues. Each database was evaluated with regards to its performance in finding references to these 155 papers.Elderly and migration were the keywords used to conduct the searches in each of the 12 databases, since these were the words that were the most frequently used in the titles of the 155 relevant articles. The search was performed in the most basic search interface of each database that allowed limiting results by the needed publication dates (1990-2000. Search results were sorted by relevance when possible (for 9 out of the 12 databases, and by date when the relevance sorting option was not available. Recall and precision statistics were then calculated from the search results. Recall is the number of relevant results obtained in the database for a search topic, divided by all the potential results which can be obtained on that topic (in this case, 155 references. Precision is the number of relevant results obtained in the database for a search topic, divided by the total number of results that were obtained in the database on

  1. Internet Databases of the Properties, Enzymatic Reactions, and Metabolism of Small Molecules—Search Options and Applications in Food Science

    Directory of Open Access Journals (Sweden)

    Piotr Minkiewicz

    2016-12-01

    Full Text Available Internet databases of small molecules, their enzymatic reactions, and metabolism have emerged as useful tools in food science. Database searching is also introduced as part of chemistry or enzymology courses for food technology students. Such resources support the search for information about single compounds and facilitate the introduction of secondary analyses of large datasets. Information can be retrieved from databases by searching for the compound name or structure, annotating with the help of chemical codes or drawn using molecule editing software. Data mining options may be enhanced by navigating through a network of links and cross-links between databases. Exemplary databases reviewed in this article belong to two classes: tools concerning small molecules (including general and specialized databases annotating food components and tools annotating enzymes and metabolism. Some problems associated with database application are also discussed. Data summarized in computer databases may be used for calculation of daily intake of bioactive compounds, prediction of metabolism of food components, and their biological activity as well as for prediction of interactions between food component and drugs.

  2. FDA Warns About Stem Cell Therapies

    Science.gov (United States)

    ... Home For Consumers Consumer Updates FDA Warns About Stem Cell Therapies Share Tweet Linkedin Pin it More sharing ... see the boxed section below for more advice. Stem Cell Uses and FDA Regulation The FDA has the ...

  3. 78 FR 14309 - Implementation of the FDA Food Safety Modernization Act Provision Requiring FDA To Establish...

    Science.gov (United States)

    2013-03-05

    ... FDA's Product Tracing Web page at http://www.fda.gov/Food/FoodSafety/FSMA/ucm270851.htm . This... Submit a Report to Congress for the Improvement of Tracking and Tracing of Food; Request for Comments and... Institute of Food Technologists (IFT) to execute product tracing pilot projects as described in the FDA Food...

  4. Decision making in family medicine: randomized trial of the effects of the InfoClinique and Trip database search engines.

    Science.gov (United States)

    Labrecque, Michel; Ratté, Stéphane; Frémont, Pierre; Cauchon, Michel; Ouellet, Jérôme; Hogg, William; McGowan, Jessie; Gagnon, Marie-Pierre; Njoya, Merlin; Légaré, France

    2013-10-01

    To compare the ability of users of 2 medical search engines, InfoClinique and the Trip database, to provide correct answers to clinical questions and to explore the perceived effects of the tools on the clinical decision-making process. Randomized trial. Three family medicine units of the family medicine program of the Faculty of Medicine at Laval University in Quebec city, Que. Fifteen second-year family medicine residents. Residents generated 30 structured questions about therapy or preventive treatment (2 questions per resident) based on clinical encounters. Using an Internet platform designed for the trial, each resident answered 20 of these questions (their own 2, plus 18 of the questions formulated by other residents, selected randomly) before and after searching for information with 1 of the 2 search engines. For each question, 5 residents were randomly assigned to begin their search with InfoClinique and 5 with the Trip database. The ability of residents to provide correct answers to clinical questions using the search engines, as determined by third-party evaluation. After answering each question, participants completed a questionnaire to assess their perception of the engine's effect on the decision-making process in clinical practice. Of 300 possible pairs of answers (1 answer before and 1 after the initial search), 254 (85%) were produced by 14 residents. Of these, 132 (52%) and 122 (48%) pairs of answers concerned questions that had been assigned an initial search with InfoClinique and the Trip database, respectively. Both engines produced an important and similar absolute increase in the proportion of correct answers after searching (26% to 62% for InfoClinique, for an increase of 36%; 24% to 63% for the Trip database, for an increase of 39%; P = .68). For all 30 clinical questions, at least 1 resident produced the correct answer after searching with either search engine. The mean (SD) time of the initial search for each question was 23.5 (7

  5. HIPdb: a database of experimentally validated HIV inhibiting peptides.

    Science.gov (United States)

    Qureshi, Abid; Thakur, Nishant; Kumar, Manoj

    2013-01-01

    Besides antiretroviral drugs, peptides have also demonstrated potential to inhibit the Human immunodeficiency virus (HIV). For example, T20 has been discovered to effectively block the HIV entry and was approved by the FDA as a novel anti-HIV peptide (AHP). We have collated all experimental information on AHPs at a single platform. HIPdb is a manually curated database of experimentally verified HIV inhibiting peptides targeting various steps or proteins involved in the life cycle of HIV e.g. fusion, integration, reverse transcription etc. This database provides experimental information of 981 peptides. These are of varying length obtained from natural as well as synthetic sources and tested on different cell lines. Important fields included are peptide sequence, length, source, target, cell line, inhibition/IC(50), assay and reference. The database provides user friendly browse, search, sort and filter options. It also contains useful services like BLAST and 'Map' for alignment with user provided sequences. In addition, predicted structure and physicochemical properties of the peptides are also included. HIPdb database is freely available at http://crdd.osdd.net/servers/hipdb. Comprehensive information of this database will be helpful in selecting/designing effective anti-HIV peptides. Thus it may prove a useful resource to researchers for peptide based therapeutics development.

  6. Efficient Similarity Search Using the Earth Mover's Distance for Large Multimedia Databases

    DEFF Research Database (Denmark)

    Assent, Ira; Wichterich, Marc; Meisen, Tobias

    2008-01-01

    Multimedia similarity search in large databases requires efficient query processing. The Earth mover's distance, introduced in computer vision, is successfully used as a similarity model in a number of small-scale applications. Its computational complexity hindered its adoption in large multimedia...... databases. We enable directly indexing the Earth mover's distance in structures such as the R-tree and the VA-file by providing the accurate 'MinDist' function to any bounding rectangle in the index. We exploit the computational structure of the new MinDist to derive a new lower bound for the EMD Min...

  7. Quantum Partial Searching Algorithm of a Database with Several Target Items

    International Nuclear Information System (INIS)

    Pu-Cha, Zhong; Wan-Su, Bao; Yun, Wei

    2009-01-01

    Choi and Korepin [Quantum Information Processing 6(2007)243] presented a quantum partial search algorithm of a database with several target items which can find a target block quickly when each target block contains the same number of target items. Actually, the number of target items in each target block is arbitrary. Aiming at this case, we give a condition to guarantee performance of the partial search algorithm to be performed and the number of queries to oracle of the algorithm to be minimized. In addition, by further numerical computing we come to the conclusion that the more uniform the distribution of target items, the smaller the number of queries

  8. Dialysis search filters for PubMed, Ovid MEDLINE, and Embase databases.

    Science.gov (United States)

    Iansavichus, Arthur V; Haynes, R Brian; Lee, Christopher W C; Wilczynski, Nancy L; McKibbon, Ann; Shariff, Salimah Z; Blake, Peter G; Lindsay, Robert M; Garg, Amit X

    2012-10-01

    Physicians frequently search bibliographic databases, such as MEDLINE via PubMed, for best evidence for patient care. The objective of this study was to develop and test search filters to help physicians efficiently retrieve literature related to dialysis (hemodialysis or peritoneal dialysis) from all other articles indexed in PubMed, Ovid MEDLINE, and Embase. A diagnostic test assessment framework was used to develop and test robust dialysis filters. The reference standard was a manual review of the full texts of 22,992 articles from 39 journals to determine whether each article contained dialysis information. Next, 1,623,728 unique search filters were developed, and their ability to retrieve relevant articles was evaluated. The high-performance dialysis filters consisted of up to 65 search terms in combination. These terms included the words "dialy" (truncated), "uremic," "catheters," and "renal transplant wait list." These filters reached peak sensitivities of 98.6% and specificities of 98.5%. The filters' performance remained robust in an independent validation subset of articles. These empirically derived and validated high-performance search filters should enable physicians to effectively retrieve dialysis information from PubMed, Ovid MEDLINE, and Embase.

  9. A searching and reporting system for relational databases using a graph-based metadata representation.

    Science.gov (United States)

    Hewitt, Robin; Gobbi, Alberto; Lee, Man-Ling

    2005-01-01

    Relational databases are the current standard for storing and retrieving data in the pharmaceutical and biotech industries. However, retrieving data from a relational database requires specialized knowledge of the database schema and of the SQL query language. At Anadys, we have developed an easy-to-use system for searching and reporting data in a relational database to support our drug discovery project teams. This system is fast and flexible and allows users to access all data without having to write SQL queries. This paper presents the hierarchical, graph-based metadata representation and SQL-construction methods that, together, are the basis of this system's capabilities.

  10. Methods and pitfalls in searching drug safety databases utilising the Medical Dictionary for Regulatory Activities (MedDRA).

    Science.gov (United States)

    Brown, Elliot G

    2003-01-01

    The Medical Dictionary for Regulatory Activities (MedDRA) is a unified standard terminology for recording and reporting adverse drug event data. Its introduction is widely seen as a significant improvement on the previous situation, where a multitude of terminologies of widely varying scope and quality were in use. However, there are some complexities that may cause difficulties, and these will form the focus for this paper. Two methods of searching MedDRA-coded databases are described: searching based on term selection from all of MedDRA and searching based on terms in the safety database. There are several potential traps for the unwary in safety searches. There may be multiple locations of relevant terms within a system organ class (SOC) and lack of recognition of appropriate group terms; the user may think that group terms are more inclusive than is the case. MedDRA may distribute terms relevant to one medical condition across several primary SOCs. If the database supports the MedDRA model, it is possible to perform multiaxial searching: while this may help find terms that might have been missed, it is still necessary to consider the entire contents of the SOCs to find all relevant terms and there are many instances of incomplete secondary linkages. It is important to adjust for multiaxiality if data are presented using primary and secondary locations. Other sources for errors in searching are non-intuitive placement and the selection of terms as preferred terms (PTs) that may not be widely recognised. Some MedDRA rules could also result in errors in data retrieval if the individual is unaware of these: in particular, the lack of multiaxial linkages for the Investigations SOC, Social circumstances SOC and Surgical and medical procedures SOC and the requirement that a PT may only be present under one High Level Term (HLT) and one High Level Group Term (HLGT) within any single SOC. Special Search Categories (collections of PTs assembled from various SOCs by

  11. Content Based Retrieval Database Management System with Support for Similarity Searching and Query Refinement

    National Research Council Canada - National Science Library

    Ortega-Binderberger, Michael

    2002-01-01

    ... as a critical area of research. This thesis explores how to enhance database systems with content based search over arbitrary abstract data types in a similarity based framework with query refinement...

  12. The DNA database search controversy revisited: bridging the Bayesian-frequentist gap.

    Science.gov (United States)

    Storvik, Geir; Egeland, Thore

    2007-09-01

    Two different quantities have been suggested for quantification of evidence in cases where a suspect is found by a search through a database of DNA profiles. The likelihood ratio, typically motivated from a Bayesian setting, is preferred by most experts in the field. The so-called np rule has been suggested through frequentist arguments and has been suggested by the American National Research Council and Stockmarr (1999, Biometrics55, 671-677). The two quantities differ substantially and have given rise to the DNA database search controversy. Although several authors have criticized the different approaches, a full explanation of why these differences appear is still lacking. In this article we show that a P-value in a frequentist hypothesis setting is approximately equal to the result of the np rule. We argue, however, that a more reasonable procedure in this case is to use conditional testing, in which case a P-value directly related to posterior probabilities and the likelihood ratio is obtained. This way of viewing the problem bridges the gap between the Bayesian and frequentist approaches. At the same time it indicates that the np rule should not be used to quantify evidence.

  13. Allie: a database and a search service of abbreviations and long forms

    Science.gov (United States)

    Yamamoto, Yasunori; Yamaguchi, Atsuko; Bono, Hidemasa; Takagi, Toshihisa

    2011-01-01

    Many abbreviations are used in the literature especially in the life sciences, and polysemous abbreviations appear frequently, making it difficult to read and understand scientific papers that are outside of a reader’s expertise. Thus, we have developed Allie, a database and a search service of abbreviations and their long forms (a.k.a. full forms or definitions). Allie searches for abbreviations and their corresponding long forms in a database that we have generated based on all titles and abstracts in MEDLINE. When a user query matches an abbreviation, Allie returns all potential long forms of the query along with their bibliographic data (i.e. title and publication year). In addition, for each candidate, co-occurring abbreviations and a research field in which it frequently appears in the MEDLINE data are displayed. This function helps users learn about the context in which an abbreviation appears. To deal with synonymous long forms, we use a dictionary called GENA that contains domain-specific terms such as gene, protein or disease names along with their synonymic information. Conceptually identical domain-specific terms are regarded as one term, and then conceptually identical abbreviation-long form pairs are grouped taking into account their appearance in MEDLINE. To keep up with new abbreviations that are continuously introduced, Allie has an automatic update system. In addition, the database of abbreviations and their long forms with their corresponding PubMed IDs is constructed and updated weekly. Database URL: The Allie service is available at http://allie.dbcls.jp/. PMID:21498548

  14. Tandem Mass Spectrum Sequencing: An Alternative to Database Search Engines in Shotgun Proteomics.

    Science.gov (United States)

    Muth, Thilo; Rapp, Erdmann; Berven, Frode S; Barsnes, Harald; Vaudel, Marc

    2016-01-01

    Protein identification via database searches has become the gold standard in mass spectrometry based shotgun proteomics. However, as the quality of tandem mass spectra improves, direct mass spectrum sequencing gains interest as a database-independent alternative. In this chapter, the general principle of this so-called de novo sequencing is introduced along with pitfalls and challenges of the technique. The main tools available are presented with a focus on user friendly open source software which can be directly applied in everyday proteomic workflows.

  15. Real-Time Ligand Binding Pocket Database Search Using Local Surface Descriptors

    Science.gov (United States)

    Chikhi, Rayan; Sael, Lee; Kihara, Daisuke

    2010-01-01

    Due to the increasing number of structures of unknown function accumulated by ongoing structural genomics projects, there is an urgent need for computational methods for characterizing protein tertiary structures. As functions of many of these proteins are not easily predicted by conventional sequence database searches, a legitimate strategy is to utilize structure information in function characterization. Of a particular interest is prediction of ligand binding to a protein, as ligand molecule recognition is a major part of molecular function of proteins. Predicting whether a ligand molecule binds a protein is a complex problem due to the physical nature of protein-ligand interactions and the flexibility of both binding sites and ligand molecules. However, geometric and physicochemical complementarity is observed between the ligand and its binding site in many cases. Therefore, ligand molecules which bind to a local surface site in a protein can be predicted by finding similar local pockets of known binding ligands in the structure database. Here, we present two representations of ligand binding pockets and utilize them for ligand binding prediction by pocket shape comparison. These representations are based on mapping of surface properties of binding pockets, which are compactly described either by the two dimensional pseudo-Zernike moments or the 3D Zernike descriptors. These compact representations allow a fast real-time pocket searching against a database. Thorough benchmark study employing two different datasets show that our representations are competitive with the other existing methods. Limitations and potentials of the shape-based methods as well as possible improvements are discussed. PMID:20455259

  16. MSblender: A probabilistic approach for integrating peptide identifications from multiple database search engines.

    Science.gov (United States)

    Kwon, Taejoon; Choi, Hyungwon; Vogel, Christine; Nesvizhskii, Alexey I; Marcotte, Edward M

    2011-07-01

    Shotgun proteomics using mass spectrometry is a powerful method for protein identification but suffers limited sensitivity in complex samples. Integrating peptide identifications from multiple database search engines is a promising strategy to increase the number of peptide identifications and reduce the volume of unassigned tandem mass spectra. Existing methods pool statistical significance scores such as p-values or posterior probabilities of peptide-spectrum matches (PSMs) from multiple search engines after high scoring peptides have been assigned to spectra, but these methods lack reliable control of identification error rates as data are integrated from different search engines. We developed a statistically coherent method for integrative analysis, termed MSblender. MSblender converts raw search scores from search engines into a probability score for every possible PSM and properly accounts for the correlation between search scores. The method reliably estimates false discovery rates and identifies more PSMs than any single search engine at the same false discovery rate. Increased identifications increment spectral counts for most proteins and allow quantification of proteins that would not have been quantified by individual search engines. We also demonstrate that enhanced quantification contributes to improve sensitivity in differential expression analyses.

  17. Validation of SmartRank: A likelihood ratio software for searching national DNA databases with complex DNA profiles.

    Science.gov (United States)

    Benschop, Corina C G; van de Merwe, Linda; de Jong, Jeroen; Vanvooren, Vanessa; Kempenaers, Morgane; Kees van der Beek, C P; Barni, Filippo; Reyes, Eusebio López; Moulin, Léa; Pene, Laurent; Haned, Hinda; Sijen, Titia

    2017-07-01

    Searching a national DNA database with complex and incomplete profiles usually yields very large numbers of possible matches that can present many candidate suspects to be further investigated by the forensic scientist and/or police. Current practice in most forensic laboratories consists of ordering these 'hits' based on the number of matching alleles with the searched profile. Thus, candidate profiles that share the same number of matching alleles are not differentiated and due to the lack of other ranking criteria for the candidate list it may be difficult to discern a true match from the false positives or notice that all candidates are in fact false positives. SmartRank was developed to put forward only relevant candidates and rank them accordingly. The SmartRank software computes a likelihood ratio (LR) for the searched profile and each profile in the DNA database and ranks database entries above a defined LR threshold according to the calculated LR. In this study, we examined for mixed DNA profiles of variable complexity whether the true donors are retrieved, what the number of false positives above an LR threshold is and the ranking position of the true donors. Using 343 mixed DNA profiles over 750 SmartRank searches were performed. In addition, the performance of SmartRank and CODIS were compared regarding DNA database searches and SmartRank was found complementary to CODIS. We also describe the applicable domain of SmartRank and provide guidelines. The SmartRank software is open-source and freely available. Using the best practice guidelines, SmartRank enables obtaining investigative leads in criminal cases lacking a suspect. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. Analysis of Users' Searches of CD-ROM Databases in the National and University Library in Zagreb.

    Science.gov (United States)

    Jokic, Maja

    1997-01-01

    Investigates the search behavior of CD-ROM database users in Zagreb (Croatia) libraries: one group needed a minimum of technical assistance, and the other was completely independent. Highlights include the use of questionnaires and transaction log analysis and the need for end-user education. The questionnaire and definitions of search process…

  19. Analysis of the Interaction between Clopidogrel, Aspirin, and Proton Pump Inhibitors Using the FDA Adverse Event Reporting System Database.

    Science.gov (United States)

    Suzuki, Yukiya; Suzuki, Honami; Umetsu, Ryogo; Uranishi, Hiroaki; Abe, Junko; Nishibata, Yuri; Sekiya, Yasuaki; Miyamura, Nobuteru; Hara, Hideaki; Tsuchiya, Teruo; Kinosada, Yasutomi; Nakamura, Mitsuhiro

    2015-01-01

    Clopidogrel is an antiplatelet agent widely used in combination with aspirin to limit the occurrence of cardiovascular (embolic/thrombotic) events. Consensus guidelines recommend proton pump inhibitors (PPIs) as a gastrointestinal (GI) prophylactic measure for all patients receiving dual antiplatelet therapy with clopidogrel and aspirin. The objective of this study was to analyze the effect of the simultaneous use of clopidogrel, aspirin, and PPIs on hemorrhagic and embolic/thrombotic events using the U.S. Food and Drug Administration (FDA) Adverse Event Reporting System (FAERS) database. Reports of hemorrhagic and embolic/thrombotic events between 2004 and 2013 were analyzed with a reporting odds ratio (ROR) algorithm and logistic regression methods. The Medical Dictionary for Regulatory Activities Preferred Terms was used to identify such events. Regarding hemorrhagic events, the adjusted RORs of the concomitant use of aspirin and clopidogrel and those of PPIs prescribed with aspirin and clopidogrel were 4.40 (95% confidence interval [CI], 4.02-4.81) and 3.40 (95% CI, 2.84-4.06), respectively. For embolic/thrombotic events, the adjusted RORs of the concomitant use of aspirin and clopidogrel and those of PPIs prescribed with aspirin and clopidogrel were 2.37 (95% CI, 2.16-2.59) and 2.38 (95% CI, 2.00-2.84), respectively. Among patients included in the FAERS database, the concurrent use of aspirin and clopidogrel with PPIs reduced the adjusted ROR of GI hemorrhagic events. PPIs had little influence on the adjusted ROR of embolic/thrombotic events. These results support the use of PPIs as a preventive measure against GI hemorrhagic events for patients receiving clopidogrel and aspirin.

  20. WAIS Searching of the Current Contents Database

    Science.gov (United States)

    Banholzer, P.; Grabenstein, M. E.

    The Homer E. Newell Memorial Library of NASA's Goddard Space Flight Center is developing capabilities to permit Goddard personnel to access electronic resources of the Library via the Internet. The Library's support services contractor, Maxima Corporation, and their subcontractor, SANAD Support Technologies have recently developed a World Wide Web Home Page (http://www-library.gsfc.nasa.gov) to provide the primary means of access. The first searchable database to be made available through the HomePage to Goddard employees is Current Contents, from the Institute for Scientific Information (ISI). The initial implementation includes coverage of articles from the last few months of 1992 to present. These records are augmented with abstracts and references, and often are more robust than equivalent records in bibliographic databases that currently serve the astronomical community. Maxima/SANAD selected Wais Incorporated's WAIS product with which to build the interface to Current Contents. This system allows access from Macintosh, IBM PC, and Unix hosts, which is an important feature for Goddard's multiplatform environment. The forms interface is structured to allow both fielded (author, article title, journal name, id number, keyword, subject term, and citation) and unfielded WAIS searches. The system allows a user to: Retrieve individual journal article records. Retrieve Table of Contents of specific issues of journals. Connect to articles with similar subject terms or keywords. Connect to other issues of the same journal in the same year. Browse journal issues from an alphabetical list of indexed journal names.

  1. Colil: a database and search service for citation contexts in the life sciences domain.

    Science.gov (United States)

    Fujiwara, Toyofumi; Yamamoto, Yasunori

    2015-01-01

    To promote research activities in a particular research area, it is important to efficiently identify current research trends, advances, and issues in that area. Although review papers in the research area can suffice for this purpose in general, researchers are not necessarily able to obtain these papers from research aspects of their interests at the time they are required. Therefore, the utilization of the citation contexts of papers in a research area has been considered as another approach. However, there are few search services to retrieve citation contexts in the life sciences domain; furthermore, efficiently obtaining citation contexts is becoming difficult due to the large volume and rapid growth of life sciences papers. Here, we introduce the Colil (Comments on Literature in Literature) database to store citation contexts in the life sciences domain. By using the Resource Description Framework (RDF) and a newly compiled vocabulary, we built the Colil database and made it available through the SPARQL endpoint. In addition, we developed a web-based search service called Colil that searches for a cited paper in the Colil database and then returns a list of citation contexts for it along with papers relevant to it based on co-citations. The citation contexts in the Colil database were extracted from full-text papers of the PubMed Central Open Access Subset (PMC-OAS), which includes 545,147 papers indexed in PubMed. These papers are distributed across 3,171 journals and cite 5,136,741 unique papers that correspond to approximately 25 % of total PubMed entries. By utilizing Colil, researchers can easily refer to a set of citation contexts and relevant papers based on co-citations for a target paper. Colil helps researchers to comprehend life sciences papers in a research area more efficiently and makes their biological research more efficient.

  2. One and done: Reasons principal investigators conduct only one FDA-regulated drug trial

    Directory of Open Access Journals (Sweden)

    Amy Corneli, PhD, MPH

    2017-06-01

    Full Text Available Concerns have been raised over the high turnover rate for clinical investigators. Using the U.S. Food and Drug Administration's (FDA Bioresearch Monitoring Information System database, we conducted an online survey to identify factors that affect principal investigators' (PIs decisions to conduct only a single FDA-regulated drug trial. Of the 201 PIs who responded, 54.2% were classified as “one-and-done.” Among these investigators, 28.9% decided for personal reasons to not conduct another trial, and 44.4% were interested in conducting another trial, but no opportunities were available. Three categories of broad barriers were identified as generally burdensome or challenging by the majority of investigators: 1 workload balance (balancing trial implementation with other work obligations and opportunities (63.8%; 2 time requirements (time to initiate and implement trial; investigator and staff time (63.4%; and 3 data and safety reporting (56.5%. Additionally, 46.0% of investigators reported being generally unsatisfied with finance-related issues. These same top three barriers also affected investigators' decisions to no longer conduct FDA-regulated trials. Our findings illuminate three key aspects of investigator turnover. First, they confirm that investigator turnover occurs, as more than half of respondents were truly “one-and-done.” Second, because a large proportion of respondents wanted to conduct more FDA-regulated trials but lacked opportunities to do so, mechanisms that match interested investigators with research sponsors are needed. Third, by focusing on the barriers we identified that affected investigators' decisions to no longer conduct FDA-regulated trials, future efforts to reduce investigator turnover can target issues that matter the most to investigators.

  3. License - Trypanosomes Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data List Contact us Trypanoso... Attribution-Share Alike 2.1 Japan . If you use data from this database, please be sure attribute this database as follows: Trypanoso...nse Update History of This Database Site Policy | Contact Us License - Trypanosomes Database | LSDB Archive ...

  4. Identification of Alternative Splice Variants Using Unique Tryptic Peptide Sequences for Database Searches.

    Science.gov (United States)

    Tran, Trung T; Bollineni, Ravi C; Strozynski, Margarita; Koehler, Christian J; Thiede, Bernd

    2017-07-07

    Alternative splicing is a mechanism in eukaryotes by which different forms of mRNAs are generated from the same gene. Identification of alternative splice variants requires the identification of peptides specific for alternative splice forms. For this purpose, we generated a human database that contains only unique tryptic peptides specific for alternative splice forms from Swiss-Prot entries. Using this database allows an easy access to splice variant-specific peptide sequences that match to MS data. Furthermore, we combined this database without alternative splice variant-1-specific peptides with human Swiss-Prot. This combined database can be used as a general database for searching of LC-MS data. LC-MS data derived from in-solution digests of two different cell lines (LNCaP, HeLa) and phosphoproteomics studies were analyzed using these two databases. Several nonalternative splice variant-1-specific peptides were found in both cell lines, and some of them seemed to be cell-line-specific. Control and apoptotic phosphoproteomes from Jurkat T cells revealed several nonalternative splice variant-1-specific peptides, and some of them showed clear quantitative differences between the two states.

  5. Identifying complications of interventional procedures from UK routine healthcare databases: a systematic search for methods using clinical codes.

    Science.gov (United States)

    Keltie, Kim; Cole, Helen; Arber, Mick; Patrick, Hannah; Powell, John; Campbell, Bruce; Sims, Andrew

    2014-11-28

    Several authors have developed and applied methods to routine data sets to identify the nature and rate of complications following interventional procedures. But, to date, there has been no systematic search for such methods. The objective of this article was to find, classify and appraise published methods, based on analysis of clinical codes, which used routine healthcare databases in a United Kingdom setting to identify complications resulting from interventional procedures. A literature search strategy was developed to identify published studies that referred, in the title or abstract, to the name or acronym of a known routine healthcare database and to complications from procedures or devices. The following data sources were searched in February and March 2013: Cochrane Methods Register, Conference Proceedings Citation Index - Science, Econlit, EMBASE, Health Management Information Consortium, Health Technology Assessment database, MathSciNet, MEDLINE, MEDLINE in-process, OAIster, OpenGrey, Science Citation Index Expanded and ScienceDirect. Of the eligible papers, those which reported methods using clinical coding were classified and summarised in tabular form using the following headings: routine healthcare database; medical speciality; method for identifying complications; length of follow-up; method of recording comorbidity. The benefits and limitations of each approach were assessed. From 3688 papers identified from the literature search, 44 reported the use of clinical codes to identify complications, from which four distinct methods were identified: 1) searching the index admission for specified clinical codes, 2) searching a sequence of admissions for specified clinical codes, 3) searching for specified clinical codes for complications from procedures and devices within the International Classification of Diseases 10th revision (ICD-10) coding scheme which is the methodology recommended by NHS Classification Service, and 4) conducting manual clinical

  6. Ten years after the FDA black box warning for antidepressant drugs: a critical narrative review

    Directory of Open Access Journals (Sweden)

    Juan Carlos Martínez-Aguayo

    2016-06-01

    Full Text Available ABSTRACT Background The United States Food and Drug Administration (FDA has warned about the increased suicidality risk associated with the use of selective serotonin reuptake inhibitors (SSRI and venlafaxine in children and adolescents. Objectives To critically appraise the available evidence supporting the FDA Black box warning concerning to the use of antidepressants in child and adolescents. Methods A critical review of articles in Medline/PubMed and SciELO databases regarding the FDA Black box warning for antidepressants, and the impact of FDA warnings on antidepressant prescriptions and suicide rates. Results The warning was based on surveys that did not report either cases of suicide nor a significant difference supporting an increased suicidality rate. The concept was defined in an ambiguous way and there is currently more available evidence to support such definition. The use of SSRI and venlafaxine has been associated to lower suicidality rates, but the prescription fall due to the warning increased suicide rates. Discussion Suicidality is an inherent feature of depressive disorders so it would be desirable to consider how much of the phenomenon may be attributed to antidepressants per se. It would be appropriate to consider that suicide rates might increase also as a consequence of the warning.

  7. Database Description - Trypanosomes Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us Trypanosomes Database Database Description General information of database Database name Trypanosomes Database...stitute of Genetics Research Organization of Information and Systems Yata 1111, Mishima, Shizuoka 411-8540, JAPAN E mail: Database...y Name: Trypanosoma Taxonomy ID: 5690 Taxonomy Name: Homo sapiens Taxonomy ID: 9606 Database description The... Article title: Author name(s): Journal: External Links: Original website information Database maintenance s...DB (Protein Data Bank) KEGG PATHWAY Database DrugPort Entry list Available Query search Available Web servic

  8. FDA approved drugs as potential Ebola treatments [v2; ref status: indexed, http://f1000r.es/554

    Directory of Open Access Journals (Sweden)

    Sean Ekins

    2015-03-01

    Full Text Available In the search for treatments for the Ebola Virus, multiple screens of FDA drugs have led to the identification of several with promising in vitro activity. These compounds were not originally developed as antivirals and some have been further tested in mouse in vivo models. We put forward the opinion that some of these drugs could be evaluated further and move into the clinic as they are already FDA approved and in many cases readily available. This may be important if there is a further outbreak in future and no other therapeutic is available.

  9. Fast quantum search algorithm for databases of arbitrary size and its implementation in a cavity QED system

    International Nuclear Information System (INIS)

    Li, H.Y.; Wu, C.W.; Liu, W.T.; Chen, P.X.; Li, C.Z.

    2011-01-01

    We propose a method for implementing the Grover search algorithm directly in a database containing any number of items based on multi-level systems. Compared with the searching procedure in the database with qubits encoding, our modified algorithm needs fewer iteration steps to find the marked item and uses the carriers of the information more economically. Furthermore, we illustrate how to realize our idea in cavity QED using Zeeman's level structure of atoms. And the numerical simulation under the influence of the cavity and atom decays shows that the scheme could be achieved efficiently within current state-of-the-art technology. -- Highlights: ► A modified Grover algorithm is proposed for searching in an arbitrary dimensional Hilbert space. ► Our modified algorithm requires fewer iteration steps to find the marked item. ► The proposed method uses the carriers of the information more economically. ► A scheme for a six-item Grover search in cavity QED is proposed. ► Numerical simulation under decays shows that the scheme can be achieved with enough fidelity.

  10. Accelerating Smith-Waterman Alignment for Protein Database Search Using Frequency Distance Filtration Scheme Based on CPU-GPU Collaborative System

    Directory of Open Access Journals (Sweden)

    Yu Liu

    2015-01-01

    Full Text Available The Smith-Waterman (SW algorithm has been widely utilized for searching biological sequence databases in bioinformatics. Recently, several works have adopted the graphic card with Graphic Processing Units (GPUs and their associated CUDA model to enhance the performance of SW computations. However, these works mainly focused on the protein database search by using the intertask parallelization technique, and only using the GPU capability to do the SW computations one by one. Hence, in this paper, we will propose an efficient SW alignment method, called CUDA-SWfr, for the protein database search by using the intratask parallelization technique based on a CPU-GPU collaborative system. Before doing the SW computations on GPU, a procedure is applied on CPU by using the frequency distance filtration scheme (FDFS to eliminate the unnecessary alignments. The experimental results indicate that CUDA-SWfr runs 9.6 times and 96 times faster than the CPU-based SW method without and with FDFS, respectively.

  11. Accelerating Smith-Waterman Alignment for Protein Database Search Using Frequency Distance Filtration Scheme Based on CPU-GPU Collaborative System.

    Science.gov (United States)

    Liu, Yu; Hong, Yang; Lin, Chun-Yuan; Hung, Che-Lun

    2015-01-01

    The Smith-Waterman (SW) algorithm has been widely utilized for searching biological sequence databases in bioinformatics. Recently, several works have adopted the graphic card with Graphic Processing Units (GPUs) and their associated CUDA model to enhance the performance of SW computations. However, these works mainly focused on the protein database search by using the intertask parallelization technique, and only using the GPU capability to do the SW computations one by one. Hence, in this paper, we will propose an efficient SW alignment method, called CUDA-SWfr, for the protein database search by using the intratask parallelization technique based on a CPU-GPU collaborative system. Before doing the SW computations on GPU, a procedure is applied on CPU by using the frequency distance filtration scheme (FDFS) to eliminate the unnecessary alignments. The experimental results indicate that CUDA-SWfr runs 9.6 times and 96 times faster than the CPU-based SW method without and with FDFS, respectively.

  12. Database Description - SKIP Stemcell Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us SKIP Stemcell Database Database Description General information of database Database name SKIP Stemcell Database...rsity Journal Search: Contact address http://www.skip.med.keio.ac.jp/en/contact/ Database classification Human Genes and Diseases Dat...abase classification Stemcell Article Organism Taxonomy Name: Homo sapiens Taxonomy ID: 9606 Database...ks: Original website information Database maintenance site Center for Medical Genetics, School of medicine, ...lable Web services Not available URL of Web services - Need for user registration Not available About This Database Database

  13. Native Health Research Database

    Science.gov (United States)

    ... Indian Health Board) Welcome to the Native Health Database. Please enter your search terms. Basic Search Advanced ... To learn more about searching the Native Health Database, click here. Tutorial Video The NHD has made ...

  14. 21 CFR 60.34 - FDA action on petitions.

    Science.gov (United States)

    2010-04-01

    ... RESTORATION Due Diligence Petitions § 60.34 FDA action on petitions. (a) Within 90 days after FDA receives a... this section or investigate and determine under § 60.36 whether the applicant acted with due diligence during the regulatory review period. FDA will publish its due diligence determination in the Federal...

  15. Impact of FDA Actions, DTCA, and Public Information on the Market for Pain Medication.

    Science.gov (United States)

    Bradford, W David; Kleit, Andrew N

    2015-07-01

    Nonsteroidal anti-inflammatory drugs (NSAIDs) are one of the most important classes of prescription drugs used by primary care physicians to manage pain. The NSAID class of products has a somewhat controversial history, around which a complex regulatory and informational environment has developed. This history includes a boxed warning mandated by the Food and Drug Administration (FDA) for all NSAIDs in 2005. We investigate the impact that various information shocks have had on the use of prescription medications for pain in primary care in the USA. We accomplish this by extracting data on nearly 600,000 patients from a unique nationwide electronic medical record database and estimate the probability of any active prescription for the four types of pain medications as a function of FDA actions, advertising, media coverage, and patient characteristics. We find that even after accounting for multiple sources of information, the FDA label changes and boxed warnings had a significant effect on pain medication prescribing. The boxed warning did not have the same impact on the use of all NSAID inhibitors. We find that the boxed warning reduced the use of NSAID COX-2 inhibitor use, which was the focus of much of the press attention. In contrast, however, the warning actually increased the use of non-COX-2 NSAID inhibitors. Thus, the efficacy of the FDA's black box warning is clearly mixed. Copyright © 2014 John Wiley & Sons, Ltd.

  16. Database Description - tRNADB-CE | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data List Contact us tRNAD...B-CE Database Description General information of database Database name tRNADB-CE Alter...CC BY-SA Detail Background and funding Name: MEXT Integrated Database Project Reference(s) Article title: tRNAD... 2009 Jan;37(Database issue):D163-8. External Links: Article title: tRNADB-CE 2011: tRNA gene database curat...n Download License Update History of This Database Site Policy | Contact Us Database Description - tRNADB-CE | LSDB Archive ...

  17. Update History of This Database - DMPD | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us DMPD Update History of This Database Date Update contents 2010/03/29 DMPD English archive si....jp/macrophage/ ) is released. About This Database Database Description Download License Update History of Thi...s Database Site Policy | Contact Us Update History of This Database - DMPD | LSDB Archive ...

  18. Quantum Query Complexity for Searching Multiple Marked States from an Unsorted Database

    International Nuclear Information System (INIS)

    Shang Bin

    2007-01-01

    An important and usual sort of search problems is to find all marked states from an unsorted database with a large number of states. Grover's original quantum search algorithm is for finding single marked state with uncertainty, and it has been generalized to the case of multiple marked states, as well as been modified to find single marked state with certainty. However, the query complexity for finding all multiple marked states has not been addressed. We use a generalized Long's algorithm with high precision to solve such a problem. We calculate the approximate query complexity, which increases with the number of marked states and with the precision that we demand. In the end we introduce an algorithm for the problem on a 'duality computer' and show its advantage over other algorithms.

  19. SimShiftDB; local conformational restraints derived from chemical shift similarity searches on a large synthetic database

    Energy Technology Data Exchange (ETDEWEB)

    Ginzinger, Simon W. [Center of Applied Molecular Engineering, University of Salzburg, Department of Molecular Biology, Division of Bioinformatics (Austria)], E-mail: simon@came.sbg.ac.at; Coles, Murray [Max-Planck-Institute for Developmental Biology, Department of Protein Evolution (Germany)], E-mail: Murray.Coles@tuebingen.mpg.de

    2009-03-15

    We present SimShiftDB, a new program to extract conformational data from protein chemical shifts using structural alignments. The alignments are obtained in searches of a large database containing 13,000 structures and corresponding back-calculated chemical shifts. SimShiftDB makes use of chemical shift data to provide accurate results even in the case of low sequence similarity, and with even coverage of the conformational search space. We compare SimShiftDB to HHSearch, a state-of-the-art sequence-based search tool, and to TALOS, the current standard tool for the task. We show that for a significant fraction of the predicted similarities, SimShiftDB outperforms the other two methods. Particularly, the high coverage afforded by the larger database often allows predictions to be made for residues not involved in canonical secondary structure, where TALOS predictions are both less frequent and more error prone. Thus SimShiftDB can be seen as a complement to currently available methods.

  20. SimShiftDB; local conformational restraints derived from chemical shift similarity searches on a large synthetic database

    International Nuclear Information System (INIS)

    Ginzinger, Simon W.; Coles, Murray

    2009-01-01

    We present SimShiftDB, a new program to extract conformational data from protein chemical shifts using structural alignments. The alignments are obtained in searches of a large database containing 13,000 structures and corresponding back-calculated chemical shifts. SimShiftDB makes use of chemical shift data to provide accurate results even in the case of low sequence similarity, and with even coverage of the conformational search space. We compare SimShiftDB to HHSearch, a state-of-the-art sequence-based search tool, and to TALOS, the current standard tool for the task. We show that for a significant fraction of the predicted similarities, SimShiftDB outperforms the other two methods. Particularly, the high coverage afforded by the larger database often allows predictions to be made for residues not involved in canonical secondary structure, where TALOS predictions are both less frequent and more error prone. Thus SimShiftDB can be seen as a complement to currently available methods

  1. Update History of This Database - RED | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us RED Update History of This Database Date Update contents 2015/12/21 Rice Expression Database English archi...s Database Database Description Download License Update History of This Database Site Policy | Contact Us Update History of This Database - RED | LSDB Archive ... ...ve site is opened. 2000/10/1 Rice Expression Database ( http://red.dna.affrc.go.jp/RED/ ) is opened. About Thi

  2. Making a search engine for Indocean - A database of abstracts: An experience

    Digital Repository Service at National Institute of Oceanography (India)

    Tapaswi, M.P.; Haravu, L.J.

    stream_size 23701 stream_content_type text/plain stream_name Inf_Manage_Trends_Issues_2003_307.pdf.txt stream_source_info Inf_Manage_Trends_Issues_2003_307.pdf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8... Information Mallagement : Trends and Issues (Festschrift ill honour of Prof S. Seetharama) 52 . Making a Search Engine for Indocean - A Database of Abstracts : An Experience Murari P Tapaswi* and L J Haravu** *Documentation Officer. National Information...

  3. Real-World Evidence, Public Participation, and the FDA.

    Science.gov (United States)

    Schwartz, Jason L

    2017-11-01

    For observers of pharmaceutical regulation and the Food and Drug Administration, these are uncertain times. Events in late 2016 raised concerns that the FDA's evidentiary standards were being weakened, compromising the agency's ability to adequately perform its regulatory and public health responsibilities. Two developments most directly contributed to these fears-the approval of eteplirsen, a treatment for Duchenne muscular dystrophy, against the recommendations of both FDA staff and an advisory committee and the December 2016 signing of the 21st Century Cures Act, which encouraged greater use by the FDA of "real-world" evidence not obtained through randomized controlled trials. The arrival of the Trump administration-with its deregulatory, industry-friendly approach-has only amplified concerns over the future of the FDA. It is too early to know whether the recent developments are truly harbingers of an FDA less likely to prevent unsafe or ineffective products from reaching the market. But elements in the two events-the role of patient narratives in deliberations regarding eteplirsen and the enthusiasm for real-world evidence in the 21st Century Cures Act-raise critical issues for the future of evidence in the FDA's work. The rigorous, inclusive approach under way to consider issues related to real-world evidence provides a model for a similarly needed inquiry regarding public participation in FDA decision-making. © 2017 The Hastings Center.

  4. Maternal characteristics associated with pregnancy exposure to FDA category C, D, and X drugs in a Canadian population.

    Science.gov (United States)

    Yang, Tubao; Walker, Mark C; Krewski, Daniel; Yang, Qiuying; Nimrod, Carl; Garner, Peter; Fraser, William; Olatunbosun, Olufemi; Wen, Shi Wu

    2008-03-01

    To estimate the frequency of exposure to prescription Food and Drug Administration (FDA) category C, D, and X drugs in pregnant women, and to analyze the maternal characteristics associated with such an exposure. A 50% random sample of women who gave a birth in Saskatchewan between January 1, 1997 and December 31, 2000 was chosen for the study. The rate of exposure to FDA category C, D, or X drugs recorded in the pharmacist database was estimated. Associations of exposure to FDA category C, D, and X drugs with maternal characteristics were evaluated using multiple logistical regression, with adjusted odds ratios (ORs) and its 95% confidence intervals (CIs) as the association measures. A total of 18 575 women were included in this study. Among them, 3604 (19.4%) had exposure to one or more FDA category C, D, and X drugs during pregnancy. Category C drugs were the most frequently used drugs (15.8%), followed by D drugs (5.2%), and X drugs (3.9%). Women with chronic health conditions had fourfold at increased risk of exposure than women without. Regardless of health status, women who were or =3, and who were on social assistance plan were at increased risk of pregnancy exposure to these drugs. About 19.4% pregnant women are exposed to FDA C, D or X drugs during pregnancy. Women with chronic diseases, younger age, increased parity, and under social assistance are at increased risk of exposure to FDA C, D, or X drugs. Copyright 2008 John Wiley & Sons, Ltd.

  5. Update History of This Database - KEGG MEDICUS | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available glish archive site is opened. 2010/10/01 KEGG MEDICUS ( http://www.kegg.jp/kegg/medicus/ ) is opened. About ...[ Credits ] English ]; } else if ( url.search(//en//) != -1 ) { url = url.replace(/...switchLanguage; BLAST Search Image Search Home About Archive Update History Data List Contact us KEGG MEDI...CUS Update History of This Database Date Update contents 2014/05/09 KEGG MEDICUS En...This Database Database Description Download License Update History of This Database Site Policy | Contact Us Update History of This Database - KEGG MEDICUS | LSDB Archive ...

  6. Update History of This Database - RPD | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us RPD Update History of This Database Date Update contents 2016/02/02 Rice Proteome Database English archi...s Database Database Description Download License Update History of This Database Site Policy | Contact Us Update History of This Database - RPD | LSDB Archive ... ...ve site is opened. 2003/01/07 Rice Proteome Database ( http://gene64.dna.affrc.go.jp/RPD/ ) is opened. About Thi

  7. Information retrieval from the INIS database. Is the new online search system poorer than the old one?

    International Nuclear Information System (INIS)

    Adamek, Petr

    2011-01-01

    A brief overview of the search options for the INIS database is presented, categorized into offline and online systems, and their assets and drawbacks are described. In the Online section, the old system on the BASIS platform and the new system on the Google Search Appliance platform are compared. The capabilities of the new system seem to be more limited than those of the old system. (author)

  8. Fine-grained Database Field Search Using Attribute-Based Encryption for E-Healthcare Clouds.

    Science.gov (United States)

    Guo, Cheng; Zhuang, Ruhan; Jie, Yingmo; Ren, Yizhi; Wu, Ting; Choo, Kim-Kwang Raymond

    2016-11-01

    An effectively designed e-healthcare system can significantly enhance the quality of access and experience of healthcare users, including facilitating medical and healthcare providers in ensuring a smooth delivery of services. Ensuring the security of patients' electronic health records (EHRs) in the e-healthcare system is an active research area. EHRs may be outsourced to a third-party, such as a community healthcare cloud service provider for storage due to cost-saving measures. Generally, encrypting the EHRs when they are stored in the system (i.e. data-at-rest) or prior to outsourcing the data is used to ensure data confidentiality. Searchable encryption (SE) scheme is a promising technique that can ensure the protection of private information without compromising on performance. In this paper, we propose a novel framework for controlling access to EHRs stored in semi-trusted cloud servers (e.g. a private cloud or a community cloud). To achieve fine-grained access control for EHRs, we leverage the ciphertext-policy attribute-based encryption (CP-ABE) technique to encrypt tables published by hospitals, including patients' EHRs, and the table is stored in the database with the primary key being the patient's unique identity. Our framework can enable different users with different privileges to search on different database fields. Differ from previous attempts to secure outsourcing of data, we emphasize the control of the searches of the fields within the database. We demonstrate the utility of the scheme by evaluating the scheme using datasets from the University of California, Irvine.

  9. Update History of This Database - SAHG | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us SAHG Update History of This Database Date Update contents 2016/05/09 SAHG English archive si...te is opened. 2009/10 SAHG ( http://bird.cbrc.jp/sahg ) is opened. About This Database Database Description ...Download License Update History of This Database Site Policy | Contact Us Update History of This Database - SAHG | LSDB Archive ...

  10. Update History of This Database - RMOS | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us RMOS Update History of This Database Date Update contents 2015/10/27 RMOS English archive si...12 RMOS (http://cdna01.dna.affrc.go.jp/RMOS/) is opened. About This Database Database Description Download License Update Hi...story of This Database Site Policy | Contact Us Update History of This Database - RMOS | LSDB Archive ...

  11. Toward a public analysis database for LHC new physics searches using M ADA NALYSIS 5

    Science.gov (United States)

    Dumont, B.; Fuks, B.; Kraml, S.; Bein, S.; Chalons, G.; Conte, E.; Kulkarni, S.; Sengupta, D.; Wymant, C.

    2015-02-01

    We present the implementation, in the MadAnalysis 5 framework, of several ATLAS and CMS searches for supersymmetry in data recorded during the first run of the LHC. We provide extensive details on the validation of our implementations and propose to create a public analysis database within this framework.

  12. GRIP Database original data - GRIPDB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data List Contact us GRI...PDB GRIP Database original data Data detail Data name GRIP Database original data DOI 10....18908/lsdba.nbdc01665-006 Description of data contents GRIP Database original data It consists of data table...s and sequences. Data file File name: gripdb_original_data.zip File URL: ftp://ftp.biosciencedbc.jp/archive/gripdb/LATEST/gri...e Database Description Download License Update History of This Database Site Policy | Contact Us GRIP Database original data - GRIPDB | LSDB Archive ...

  13. Update History of This Database - PLACE | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us PLACE Update History of This Database Date Update contents 2016/08/22 The contact address is...s Database Database Description Download License Update History of Thi...s Database Site Policy | Contact Us Update History of This Database - PLACE | LSDB Archive ... ... changed. 2014/10/20 The URLs of the database maintenance site and the portal site are changed. 2014/07/17 PLACE English archi

  14. Update History of This Database - SSBD | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us SSBD Update History of This Database Date Update contents 2016/07/25 SSBD English archive si...tion Download License Update History of This Database Site Policy | Contact Us Update History of This Database - SSBD | LSDB Archive ... ...te is opened. 2013/09/03 SSBD ( http://ssbd.qbic.riken.jp/ ) is opened. About This Database Database Descrip

  15. EVA geen FDA

    NARCIS (Netherlands)

    Folbert, J.P.; Dagevos, J.C.

    2001-01-01

    De oprichting van een Europese Voedselautoriteit die in 2002 operationeel moet zijn. Velen zien hierin een evenbeeld van de Amerikaanse FDA (Food and Drug Administration). Deze instantie werkt echter niet zo ideaal als vaak wordt voorgesteld. Het belangrijkste verschil tussen beide instanties is de

  16. Oracle Database 10g: a platform for BLAST search and Regular Expression pattern matching in life sciences.

    Science.gov (United States)

    Stephens, Susie M; Chen, Jake Y; Davidson, Marcel G; Thomas, Shiby; Trute, Barry M

    2005-01-01

    As database management systems expand their array of analytical functionality, they become powerful research engines for biomedical data analysis and drug discovery. Databases can hold most of the data types commonly required in life sciences and consequently can be used as flexible platforms for the implementation of knowledgebases. Performing data analysis in the database simplifies data management by minimizing the movement of data from disks to memory, allowing pre-filtering and post-processing of datasets, and enabling data to remain in a secure, highly available environment. This article describes the Oracle Database 10g implementation of BLAST and Regular Expression Searches and provides case studies of their usage in bioinformatics. http://www.oracle.com/technology/software/index.html.

  17. Protein backbone angle restraints from searching a database for chemical shift and sequence homology

    Energy Technology Data Exchange (ETDEWEB)

    Cornilescu, Gabriel; Delaglio, Frank; Bax, Ad [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)

    1999-03-15

    Chemical shifts of backbone atoms in proteins are exquisitely sensitive to local conformation, and homologous proteins show quite similar patterns of secondary chemical shifts. The inverse of this relation is used to search a database for triplets of adjacent residues with secondary chemical shifts and sequence similarity which provide the best match to the query triplet of interest. The database contains 13C{alpha}, 13C{beta}, 13C', 1H{alpha} and 15N chemical shifts for 20 proteins for which a high resolution X-ray structure is available. The computer program TALOS was developed to search this database for strings of residues with chemical shift and residue type homology. The relative importance of the weighting factors attached to the secondary chemical shifts of the five types of resonances relative to that of sequence similarity was optimized empirically. TALOS yields the 10 triplets which have the closest similarity in secondary chemical shift and amino acid sequence to those of the query sequence. If the central residues in these 10 triplets exhibit similar {phi} and {psi} backbone angles, their averages can reliably be used as angular restraints for the protein whose structure is being studied. Tests carried out for proteins of known structure indicate that the root-mean-square difference (rmsd) between the output of TALOS and the X-ray derived backbone angles is about 15 deg. Approximately 3% of the predictions made by TALOS are found to be in error.

  18. Identifying and Synchronizing Health Information Technology (HIT) Events from FDA Medical Device Reports.

    Science.gov (United States)

    Kang, Hong; Wang, Frank; Zhou, Sicheng; Miao, Qi; Gong, Yang

    2017-01-01

    Health information technology (HIT) events, a subtype of patient safety events, pose a major threat and barrier toward a safer healthcare system. It is crucial to gain a better understanding of the nature of the errors and adverse events caused by current HIT systems. The scarcity of HIT event-exclusive databases and event reporting systems indicates the challenge of identifying the HIT events from existing resources. FDA Manufacturer and User Facility Device Experience (MAUDE) database is a potential resource for HIT events. However, the low proportion and the rapid evolvement of HIT-related events present challenges for distinguishing them from other equipment failures and hazards. We proposed a strategy to identify and synchronize HIT events from MAUDE by using a filter based on structured features and classifiers based on unstructured features. The strategy will help us develop and grow an HIT event-exclusive database, keeping pace with updates to MAUDE toward shared learning.

  19. FDA and the Chemical Brain Drainers

    DEFF Research Database (Denmark)

    Grandjean, Philippe

    2017-01-01

    Comment to: "Anesthesia and Developing Brains — Implications of the FDA Warning." Dean B. Andropoulos, M.D., M.H.C.M., and Michael F. Greene, M.D. N Engl J Med 2017; 376:905-907......Comment to: "Anesthesia and Developing Brains — Implications of the FDA Warning." Dean B. Andropoulos, M.D., M.H.C.M., and Michael F. Greene, M.D. N Engl J Med 2017; 376:905-907...

  20. Database Description - ASTRA | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available abase Description General information of database Database name ASTRA Alternative n...tics Journal Search: Contact address Database classification Nucleotide Sequence Databases - Gene structure,...3702 Taxonomy Name: Oryza sativa Taxonomy ID: 4530 Database description The database represents classified p...(10):1211-6. External Links: Original website information Database maintenance site National Institute of Ad... for user registration Not available About This Database Database Description Dow

  1. Database Description - TMFunction | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available sidue (or mutant) in a protein. The experimental data are collected from the literature both by searching th...the sequence database, UniProt, structural database, PDB, and literature database

  2. Update History of This Database - fRNAdb | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us fRNAdb Update History of This Database Date Update contents 2016/03/29 fRNAdb English archiv...on Download License Update History of This Database Site Policy | Contact Us Update History of This Database - fRNAdb | LSDB Archive ... ...e site is opened. 2006/12 fRNAdb ( http://www.ncrna.org/ ) is opened. About This Database Database Descripti

  3. Literature searches on Ayurveda: An update.

    Science.gov (United States)

    Aggithaya, Madhur G; Narahari, Saravu R

    2015-01-01

    The journals that publish on Ayurveda are increasingly indexed by popular medical databases in recent years. However, many Eastern journals are not indexed biomedical journal databases such as PubMed. Literature searches for Ayurveda continue to be challenging due to the nonavailability of active, unbiased dedicated databases for Ayurvedic literature. In 2010, authors identified 46 databases that can be used for systematic search of Ayurvedic papers and theses. This update reviewed our previous recommendation and identified current and relevant databases. To update on Ayurveda literature search and strategy to retrieve maximum publications. Author used psoriasis as an example to search previously listed databases and identify new. The population, intervention, control, and outcome table included keywords related to psoriasis and Ayurvedic terminologies for skin diseases. Current citation update status, search results, and search options of previous databases were assessed. Eight search strategies were developed. Hundred and five journals, both biomedical and Ayurveda, which publish on Ayurveda, were identified. Variability in databases was explored to identify bias in journal citation. Five among 46 databases are now relevant - AYUSH research portal, Annotated Bibliography of Indian Medicine, Digital Helpline for Ayurveda Research Articles (DHARA), PubMed, and Directory of Open Access Journals. Search options in these databases are not uniform, and only PubMed allows complex search strategy. "The Researches in Ayurveda" and "Ayurvedic Research Database" (ARD) are important grey resources for hand searching. About 44/105 (41.5%) journals publishing Ayurvedic studies are not indexed in any database. Only 11/105 (10.4%) exclusive Ayurveda journals are indexed in PubMed. AYUSH research portal and DHARA are two major portals after 2010. It is mandatory to search PubMed and four other databases because all five carry citations from different groups of journals. The hand

  4. 21 CFR 60.10 - FDA assistance on eligibility.

    Science.gov (United States)

    2010-04-01

    ... from the U.S. Patent and Trademark Office, FDA will assist the U.S. Patent and Trademark Office in... in FDA's Division of Dockets Management (HFA-305), 5630 Fishers Lane, rm. 1061, Rockville, MD 20852...

  5. Specialist Bibliographic Databases.

    Science.gov (United States)

    Gasparyan, Armen Yuri; Yessirkepov, Marlen; Voronov, Alexander A; Trukhachev, Vladimir I; Kostyukova, Elena I; Gerasimov, Alexey N; Kitas, George D

    2016-05-01

    Specialist bibliographic databases offer essential online tools for researchers and authors who work on specific subjects and perform comprehensive and systematic syntheses of evidence. This article presents examples of the established specialist databases, which may be of interest to those engaged in multidisciplinary science communication. Access to most specialist databases is through subscription schemes and membership in professional associations. Several aggregators of information and database vendors, such as EBSCOhost and ProQuest, facilitate advanced searches supported by specialist keyword thesauri. Searches of items through specialist databases are complementary to those through multidisciplinary research platforms, such as PubMed, Web of Science, and Google Scholar. Familiarizing with the functional characteristics of biomedical and nonbiomedical bibliographic search tools is mandatory for researchers, authors, editors, and publishers. The database users are offered updates of the indexed journal lists, abstracts, author profiles, and links to other metadata. Editors and publishers may find particularly useful source selection criteria and apply for coverage of their peer-reviewed journals and grey literature sources. These criteria are aimed at accepting relevant sources with established editorial policies and quality controls.

  6. Specialist Bibliographic Databases

    Science.gov (United States)

    2016-01-01

    Specialist bibliographic databases offer essential online tools for researchers and authors who work on specific subjects and perform comprehensive and systematic syntheses of evidence. This article presents examples of the established specialist databases, which may be of interest to those engaged in multidisciplinary science communication. Access to most specialist databases is through subscription schemes and membership in professional associations. Several aggregators of information and database vendors, such as EBSCOhost and ProQuest, facilitate advanced searches supported by specialist keyword thesauri. Searches of items through specialist databases are complementary to those through multidisciplinary research platforms, such as PubMed, Web of Science, and Google Scholar. Familiarizing with the functional characteristics of biomedical and nonbiomedical bibliographic search tools is mandatory for researchers, authors, editors, and publishers. The database users are offered updates of the indexed journal lists, abstracts, author profiles, and links to other metadata. Editors and publishers may find particularly useful source selection criteria and apply for coverage of their peer-reviewed journals and grey literature sources. These criteria are aimed at accepting relevant sources with established editorial policies and quality controls. PMID:27134485

  7. Statistical Measures Alone Cannot Determine Which Database (BNI, CINAHL, MEDLINE, or EMBASE Is the Most Useful for Searching Undergraduate Nursing Topics. A Review of: Stokes, P., Foster, A., & Urquhart, C. (2009. Beyond relevance and recall: Testing new user-centred measures of database performance. Health Information and Libraries Journal, 26(3, 220-231.

    Directory of Open Access Journals (Sweden)

    Giovanna Badia

    2011-03-01

    Full Text Available Objective – The research project sought to determine which of four databases was the most useful for searching undergraduate nursing topics. Design – Comparative database evaluation. Setting – Nursing and midwifery students at Homerton School of Health Studies (now part of Anglia Ruskin University, Cambridge, United Kingdom, in 2005-2006. Subjects – The subjects were four databases: British Nursing Index (BNI, CINAHL, MEDLINE, and EMBASE.Methods – This was a comparative study using title searches to compare BNI (BritishNursing Index, CINAHL, MEDLINE and EMBASE.According to the authors, this is the first study to compare BNI with other databases. BNI is a database produced by British libraries that indexes the nursing and midwifery literature. It covers over 240 British journals, and includes references to articles from health sciences journals that are relevant to nurses and midwives (British Nursing Index, n.d..The researchers performed keyword searches in the title field of the four databases for the dissertation topics of nine nursing and midwifery students enrolled in undergraduate dissertation modules. The list of titles of journals articles on their topics were given to the students and they were asked to judge the relevancy of the citations. The title searches were evaluated in each of the databases using the following criteria: • precision (the number of relevant results obtained in the database for a search topic, divided by the total number of results obtained in the database search;• recall (the number of relevant results obtained in the database for a search topic, divided by the total number of relevant results obtained on that topic from all four database searches;• novelty (the number of relevant results that were unique in the database search, which was calculated as a percentage of the total number of relevant results found in the database;• originality (the number of unique relevant results obtained in the

  8. Update History of This Database - TogoTV | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us TogoTV Update History of This Database Date Update contents 2017/05/12 TogoTV English archiv...ription Download License Update History of This Database Site Policy | Contact Us Update History of This Database - TogoTV | LSDB Archive ... ...e site is opened. 2007/07/20 TogoTV ( http://togotv.dbcls.jp/ ) is opened. About This Database Database Desc

  9. Update History of This Database - ConfC | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us ConfC Update History of This Database Date Update contents 2016/09/20 ConfC English archive ...tion Download License Update History of This Database Site Policy | Contact Us Update History of This Database - ConfC | LSDB Archive ... ...site is opened. 2005/05/01 ConfC (http://mbs.cbrc.jp/ConfC/) is opened. About This Database Database Descrip

  10. Matrix-product-state simulation of an extended Brueschweiler bulk-ensemble database search

    International Nuclear Information System (INIS)

    SaiToh, Akira; Kitagawa, Masahiro

    2006-01-01

    Brueschweiler's database search in a spin Liouville space can be efficiently simulated on a conventional computer without error as long as the simulation cost of the internal circuit of an oracle function is polynomial, unlike the fact that in true NMR experiments, it suffers from an exponential decrease in the variation of a signal intensity. With the simulation method using the matrix-product-state proposed by Vidal [G. Vidal, Phys. Rev. Lett. 91, 147902 (2003)], we perform such a simulation. We also show the extensions of the algorithm without utilizing the J-coupling or DD-coupling splitting of frequency peaks in observation: searching can be completed with a single query in polynomial postoracle circuit complexities in an extension; multiple solutions of an oracle can be found in another extension whose query complexity is linear in the key length and in the number of solutions (this extension is to find all of marked keys). These extended algorithms are also simulated with the same simulation method

  11. Protein structure determination by exhaustive search of Protein Data Bank derived databases.

    Science.gov (United States)

    Stokes-Rees, Ian; Sliz, Piotr

    2010-12-14

    Parallel sequence and structure alignment tools have become ubiquitous and invaluable at all levels in the study of biological systems. We demonstrate the application and utility of this same parallel search paradigm to the process of protein structure determination, benefitting from the large and growing corpus of known structures. Such searches were previously computationally intractable. Through the method of Wide Search Molecular Replacement, developed here, they can be completed in a few hours with the aide of national-scale federated cyberinfrastructure. By dramatically expanding the range of models considered for structure determination, we show that small (less than 12% structural coverage) and low sequence identity (less than 20% identity) template structures can be identified through multidimensional template scoring metrics and used for structure determination. Many new macromolecular complexes can benefit significantly from such a technique due to the lack of known homologous protein folds or sequences. We demonstrate the effectiveness of the method by determining the structure of a full-length p97 homologue from Trichoplusia ni. Example cases with the MHC/T-cell receptor complex and the EmoB protein provide systematic estimates of minimum sequence identity, structure coverage, and structural similarity required for this method to succeed. We describe how this structure-search approach and other novel computationally intensive workflows are made tractable through integration with the US national computational cyberinfrastructure, allowing, for example, rapid processing of the entire Structural Classification of Proteins protein fragment database.

  12. Download - Trypanosomes Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us Trypanosomes Database Download First of all, please read the license of this database. Data ...1.4 KB) Simple search and download Downlaod via FTP FTP server is sometimes jammed. If it is, access [here]. About This Database Data...base Description Download License Update History of This Database Site Policy | Contact Us Download - Trypanosomes Database | LSDB Archive ...

  13. Update History of This Database - RMG | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us RMG Update History of This Database Date Update contents 2016/08/22 The contact address is c...dna.affrc.go.jp/ ) is opened. About This Database Database Description Download License Update Hi...story of This Database Site Policy | Contact Us Update History of This Database - RMG | LSDB Archive ... ... URL of the portal site is changed. 2013/08/07 RMG archive site is opened. 2002/09/25 RMG ( http://rmg.rice.

  14. Update History of This Database - DGBY | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us DGBY Update History of This Database Date Update contents 2014/10/20 The URL of the portal s...aro.affrc.go.jp/yakudachi/yeast/index.html ) is opened. About This Database Database Description Download License Update Hi...story of This Database Site Policy | Contact Us Update History of This Database - DGBY | LSDB Archive ... ... Expression of attribution in License is updated. 2012/03/08 DGBY English archive site is opened. 2006/10/02

  15. Update History of This Database - KAIKOcDNA | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us KAIKOcDNA Update History of This Database Date Update contents 2014/10/20 The URL of the dat... database ( http://sgp.dna.affrc.go.jp/EST/ ) is opened. About This Database Database Description Download License Update Hi...story of This Database Site Policy | Contact Us Update History of This Database - KAIKOcDNA | LSDB Archive ... ...abase maintenance site is changed. 2014/10/08 KAIKOcDNA English archive site is opened. 2004/04/12 KAIKOcDNA

  16. Update History of This Database - AcEST | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us AcEST Update History of This Database Date Update contents 2013/01/10 Errors found on AcEST ...s Database Database Description Download License Update History of This Data...base Site Policy | Contact Us Update History of This Database - AcEST | LSDB Archive ... ...Conting data have been correceted. For details, please refer to the following page. Data correction 2010/03/29 AcEST English archi

  17. Agreements and Discrepancies between FDA Reports and Journal Papers on Biologic Agents Approved for Rheumatoid Arthritis: A Meta-Research Project.

    Directory of Open Access Journals (Sweden)

    Gil Amarilyo

    Full Text Available Sponsors that seek to commercialize new drugs apply to the Food and Drug Administration (FDA which independently analyzes the raw data and reports the results on its website.This study sought to determine if there are differences between the FDA assessments and journal reports on biologic agents developed for the treatment of rheumatoid arthritis.Available data on FDA-approved drugs were extracted from the website, and a systematic literature search was conducted to identify matching studies in peer-reviewed medical journals. Outcome measures were the American College of Rheumatology response criteria ACR20 (efficacy and withdrawal due to adverse events (safety. As effect size odds ratios were estimated for each active trial arm vs. control arm (i.e. for both sources: FDA and journal report, followed by calculation of the ratios of the FDA and journal report odds ratios. A ratio of odds ratios not equal to 1 was categorized as a discrepancy.FDA reports were available for 8 of 9 FDA-approved biologic agents for rheumatoid arthritis; all identified trials (34 except one were published in peer-reviewed journals. Overall, discrepancies were noted for 20 of the 33 evaluated trials. Differences in the apparent benefit reporting were found in 39% (24/61 pairwise comparisons and in 11 cases these were statistically significant; the FDA report showed greater benefit than the journal publication in 15 comparisons and lesser benefit in 9. Differences in the reported harms were found in 51% (28/55 pairwise comparisons and were statistically significant in 5. The "signal" in FDA reports showed a less harmful effect than the journal publication in 17 comparisons whereas a more harmful effect in 11. The differences were attributed to differences in analytic approach, patient inclusion, rounding effect, and counting discrepancies. However, no differences were categorized as critical.There was no empirical evidence to suggest biased estimates between the two

  18. Changes In Growth Culture FDA Activity Under Changing Growth Conditions

    DEFF Research Database (Denmark)

    Jørgensen, Per Elberg; Eriksen, Thomas Juul; Jensen, Bjørn K.

    1992-01-01

    The FDA hydrolysis capacities and bacterial biomass concentrations (estimated by determination of ATP content) of growth cultures prepared from activated sludge and wastewater, were measured to find out whether the FDA activity would reflect bacterial biomass under different physiological states...... of the bacteria. The FDA activity/ATP ratio was calculated for different concentrations of autoclaved sludge. A faster decay rate of ATP relative to FDA hydrolysis activity was observed, thus causing changes in the ratio. Furthermore, comparison between values obtained from pure cultures and different soils...... revealed differences up to two orders of magnitude of the ratio. Based on these results it was concluded that the FDA activity should not be applied for measurements of viable biomass in environments in which different physiological conditions occur....

  19. A common feature pharmacophore for FDA-approved drugs inhibiting the Ebola virus.

    Science.gov (United States)

    Ekins, Sean; Freundlich, Joel S; Coffee, Megan

    2014-01-01

    We are currently faced with a global infectious disease crisis which has been anticipated for decades. While many promising biotherapeutics are being tested, the search for a small molecule has yet to deliver an approved drug or therapeutic for the Ebola or similar filoviruses that cause haemorrhagic fever. Two recent high throughput screens published in 2013 did however identify several hits that progressed to animal studies that are FDA approved drugs used for other indications. The current computational analysis uses these molecules from two different structural classes to construct a common features pharmacophore. This ligand-based pharmacophore implicates a possible common target or mechanism that could be further explored. A recent structure based design project yielded nine co-crystal structures of pyrrolidinone inhibitors bound to the viral protein 35 (VP35). When receptor-ligand pharmacophores based on the analogs of these molecules and the protein structures were constructed, the molecular features partially overlapped with the common features of solely ligand-based pharmacophore models based on FDA approved drugs. These previously identified FDA approved drugs with activity against Ebola were therefore docked into this protein. The antimalarials chloroquine and amodiaquine docked favorably in VP35. We propose that these drugs identified to date as inhibitors of the Ebola virus may be targeting VP35. These computational models may provide preliminary insights into the molecular features that are responsible for their activity against Ebola virus in vitro and in vivo and we propose that this hypothesis could be readily tested.

  20. The Relationship between Searches Performed in Online Databases and the Number of Full-Text Articles Accessed: Measuring the Interaction between Database and E-Journal Collections

    Science.gov (United States)

    Lamothe, Alain R.

    2011-01-01

    The purpose of this paper is to report the results of a quantitative analysis exploring the interaction and relationship between the online database and electronic journal collections at the J. N. Desmarais Library of Laurentian University. A very strong relationship exists between the number of searches and the size of the online database…

  1. Subarray-based FDA radar to counteract deceptive ECM signals

    Science.gov (United States)

    Abdalla, Ahmed; Wang, Wen-Qin; Yuan, Zhao; Mohamed, Suhad; Bin, Tang

    2016-12-01

    In recent years, the frequency diverse array (FDA) radar concept has attracted extensive attention, as it may benefit from a small frequency increment, compared to the carrier frequency across the array elements and thereby achieve an array factor that is a function of the angle, the time, and the range which is superior to the conventional phase array radar (PAR). However, limited effort on the subject of FDA in electronic countermeasure scenarios, especially in the presence of mainbeam deceptive jamming, has been published. Basic FDA is not desirable for anti-jamming applications, due to the range-angle coupling response of targets. In this paper, a novel method based on subarrayed FDA signal processing is proposed to counteract deceptive ECM signals. We divide the FDA array into multiple subarrays, each of which employs a distinct frequency increment. As a result, in the subarray-based FDA, the desired target can be distinguished at subarray level in joint range-angle-Doppler domain by utilizing the fact that the jammer generates false targets with the same ranges to each subarray without reparations. The performance assessment shows that the proposed solution is effective for deceptive ECM targets suppression. The effectiveness is verified by simulation results.

  2. The VirusBanker database uses a Java program to allow flexible searching through Bunyaviridae sequences.

    Science.gov (United States)

    Fourment, Mathieu; Gibbs, Mark J

    2008-02-05

    Viruses of the Bunyaviridae have segmented negative-stranded RNA genomes and several of them cause significant disease. Many partial sequences have been obtained from the segments so that GenBank searches give complex results. Sequence databases usually use HTML pages to mediate remote sorting, but this approach can be limiting and may discourage a user from exploring a database. The VirusBanker database contains Bunyaviridae sequences and alignments and is presented as two spreadsheets generated by a Java program that interacts with a MySQL database on a server. Sequences are displayed in rows and may be sorted using information that is displayed in columns and includes data relating to the segment, gene, protein, species, strain, sequence length, terminal sequence and date and country of isolation. Bunyaviridae sequences and alignments may be downloaded from the second spreadsheet with titles defined by the user from the columns, or viewed when passed directly to the sequence editor, Jalview. VirusBanker allows large datasets of aligned nucleotide and protein sequences from the Bunyaviridae to be compiled and winnowed rapidly using criteria that are formulated heuristically.

  3. Integration of first-principles methods and crystallographic database searches for new ferroelectrics: Strategies and explorations

    International Nuclear Information System (INIS)

    Bennett, Joseph W.; Rabe, Karin M.

    2012-01-01

    In this concept paper, the development of strategies for the integration of first-principles methods with crystallographic database mining for the discovery and design of novel ferroelectric materials is discussed, drawing on the results and experience derived from exploratory investigations on three different systems: (1) the double perovskite Sr(Sb 1/2 Mn 1/2 )O 3 as a candidate semiconducting ferroelectric; (2) polar derivatives of schafarzikite MSb 2 O 4 ; and (3) ferroelectric semiconductors with formula M 2 P 2 (S,Se) 6 . A variety of avenues for further research and investigation are suggested, including automated structure type classification, low-symmetry improper ferroelectrics, and high-throughput first-principles searches for additional representatives of structural families with desirable functional properties. - Graphical abstract: Integration of first-principles methods with crystallographic database mining, for the discovery and design of novel ferroelectric materials, could potentially lead to new classes of multifunctional materials. Highlights: ► Integration of first-principles methods and database mining. ► Minor structural families with desirable functional properties. ► Survey of polar entries in the Inorganic Crystal Structural Database.

  4. Social Work Literature Searching: Current Issues with Databases and Online Search Engines

    Science.gov (United States)

    McGinn, Tony; Taylor, Brian; McColgan, Mary; McQuilkan, Janice

    2016-01-01

    Objectives: To compare the performance of a range of search facilities; and to illustrate the execution of a comprehensive literature search for qualitative evidence in social work. Context: Developments in literature search methods and comparisons of search facilities help facilitate access to the best available evidence for social workers.…

  5. Pharmacovigilance database search discloses ClC-K channels as a novel target of the AT1 receptor blockers valsartan and olmesartan.

    Science.gov (United States)

    Imbrici, Paola; Tricarico, Domenico; Mangiatordi, Giuseppe Felice; Nicolotti, Orazio; Lograno, Marcello Diego; Conte, Diana; Liantonio, Antonella

    2017-07-01

    Human ClC-K chloride channels are highly attractive targets for drug discovery as they have a variety of important physiological functions and are associated with genetic disorders. These channels are crucial in the kidney as they control chloride reabsorption and water diuresis. In addition, loss-of-function mutations of CLCNKB and BSND genes cause Bartter's syndrome (BS), whereas CLCNKA and CLCNKB gain-of-function polymorphisms predispose to a rare form of salt sensitive hypertension. Both disorders lack a personalized therapy that is in most cases only symptomatic. The aim of this study was to identify novel ClC-K ligands from drugs already on the market, by exploiting the pharmacological side activity of drug molecules available from the FDA Adverse Effects Reporting System database. We searched for drugs having a Bartter-like syndrome as a reported side effect, with the assumption that BS could be causatively related to the block of ClC-K channels. The ability of the selected BS-causing drugs to bind and block ClC-K channels was then validated through an integrated experimental and computational approach based on patch clamp electrophysiology in HEK293 cells and molecular docking simulations. Valsartan and olmesartan were able to block ClC-Ka channels and the molecular requirements for effective inhibition of these channels have been identified. These results suggest additional mechanisms of action for these sartans further to their primary AT 1 receptor antagonism and propose these compounds as leads for designing new potent ClC-K ligands. © 2017 The British Pharmacological Society.

  6. Accessing and using chemical databases

    DEFF Research Database (Denmark)

    Nikolov, Nikolai Georgiev; Pavlov, Todor; Niemelä, Jay Russell

    2013-01-01

    Computer-based representation of chemicals makes it possible to organize data in chemical databases-collections of chemical structures and associated properties. Databases are widely used wherever efficient processing of chemical information is needed, including search, storage, retrieval......, and dissemination. Structure and functionality of chemical databases are considered. The typical kinds of information found in a chemical database are considered-identification, structural, and associated data. Functionality of chemical databases is presented, with examples of search and access types. More details...... are included about the OASIS database and platform and the Danish (Q)SAR Database online. Various types of chemical database resources are discussed, together with a list of examples....

  7. Regulating nanomedicine - can the FDA handle it?

    Science.gov (United States)

    Bawa, Raj

    2011-05-01

    There is enormous excitement and expectation surrounding the multidisciplinary field of nanomedicine - the application of nanotechnology to healthcare - which is already influencing the pharmaceutical industry. This is especially true in the design, formulation and delivery of therapeutics. Currently, nanomedicine is poised at a critical stage. However, regulatory guidance in this area is generally lacking and critically needed to provide clarity and legal certainty to manufacturers, policymakers, healthcare providers as well as public. There are hundreds, if not thousands, of nanoproducts on the market for human use but little is known of their health risks, safety data and toxicity profiles. Less is known of nanoproducts that are released into the environment and that come in contact with humans. These nanoproducts, whether they are a drug, device, biologic or combination of any of these, are creating challenges for the Food and Drug Administration (FDA), as regulators struggle to accumulate data and formulate testing criteria to ensure development of safe and efficacious nanoproducts (products incorporating nanoscale technologies). Evidence continues to mount that many nanoproducts inherently posses novel size-based properties and toxicity profiles. Yet, this scientific fact has been generally ignored by the FDA and the agency continues to adopt a precautionary approach to the issue in hopes of countering future potential negative public opinion. As a result, the FDA has simply maintained the status quo with regard to its regulatory policies pertaining to nanomedicine. Therefore, there are no specific laws or mechanisms in place for oversight of nanomedicine and the FDA continues to treat nanoproducts as substantially equivalent ("bioequivalent") to their bulk counterparts. So, for now nanoproducts submitted for FDA review will continue to be subjected to an uncertain regulatory pathway. Such regulatory uncertainty could negatively impact venture funding, stifle

  8. Update History of This Database - TP Atlas | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us TP Atlas Update History of This Database Date Update contents 2013/12/16 The email address i...s ( http://www.tanpaku.org/tpatlas/ ) is opened. About This Database Database Description Download License Update History of Thi...s Database Site Policy | Contact Us Update History of This Database - TP Atlas | LSDB Archive ... ...n the contact information is corrected. 2013/11/19 TP Atlas English archive site is opened. 2008/4/1 TP Atla

  9. Update History of This Database - GenLibi | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us GenLibi Update History of This Database Date Update contents 2014/03/25 GenLibi English archi...base Description Download License Update History of This Database Site Policy | Contact Us Update History of This Database - GenLibi | LSDB Archive ... ...ve site is opened. 2007/03/01 GenLibi ( http://gene.biosciencedbc.jp/ ) is opened. About This Database Data

  10. Update History of This Database - dbQSNP | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us dbQSNP Update History of This Database Date Update contents 2017/02/16 dbQSNP English archiv...e Description Download License Update History of This Database Site Policy | Contact Us Update History of This Database - dbQSNP | LSDB Archive ... ...e site is opened. 2002/10/23 dbQSNP (http://qsnp.gen.kyushu-u.ac.jp/) is opened. About This Database Databas

  11. Database with web interface and search engine as a diagnostics tool for electromagnetic calorimeter

    CERN Document Server

    Paluoja, Priit

    2017-01-01

    During 2016 data collection, the Compact Muon Solenoid Data Acquisition (CMS DAQ) system has shown a very good reliability. Nevertheless, the high complexity of the hardware and the software involved is, by its nature, prone to some occasional problems. As CMS subdetector, electromagnetic calorimeter (ECAL) is affected in the same way. Some of the issues are not predictable and can appear during the year more than once such as components getting noisy, power shortcuts or failing communication between machines. The chain detection-diagnosis-intervention must be as fast as possible to minimise the downtime of the detector. The aim of this project was to create a diagnostic software for ECAL crew, which consists of database and its web interface that allows to search, add and edit the contents of the database.

  12. The Magnetics Information Consortium (MagIC) Online Database: Uploading, Searching and Visualizing Paleomagnetic and Rock Magnetic Data

    Science.gov (United States)

    Minnett, R.; Koppers, A.; Tauxe, L.; Constable, C.; Pisarevsky, S. A.; Jackson, M.; Solheid, P.; Banerjee, S.; Johnson, C.

    2006-12-01

    The Magnetics Information Consortium (MagIC) is commissioned to implement and maintain an online portal to a relational database populated by both rock and paleomagnetic data. The goal of MagIC is to archive all measurements and the derived properties for studies of paleomagnetic directions (inclination, declination) and intensities, and for rock magnetic experiments (hysteresis, remanence, susceptibility, anisotropy). MagIC is hosted under EarthRef.org at http://earthref.org/MAGIC/ and has two search nodes, one for paleomagnetism and one for rock magnetism. Both nodes provide query building based on location, reference, methods applied, material type and geological age, as well as a visual map interface to browse and select locations. The query result set is displayed in a digestible tabular format allowing the user to descend through hierarchical levels such as from locations to sites, samples, specimens, and measurements. At each stage, the result set can be saved and, if supported by the data, can be visualized by plotting global location maps, equal area plots, or typical Zijderveld, hysteresis, and various magnetization and remanence diagrams. User contributions to the MagIC database are critical to achieving a useful research tool. We have developed a standard data and metadata template (Version 2.1) that can be used to format and upload all data at the time of publication in Earth Science journals. Software tools are provided to facilitate population of these templates within Microsoft Excel. These tools allow for the import/export of text files and provide advanced functionality to manage and edit the data, and to perform various internal checks to maintain data integrity and prepare for uploading. The MagIC Contribution Wizard at http://earthref.org/MAGIC/upload.htm executes the upload and takes only a few minutes to process several thousand data records. The standardized MagIC template files are stored in the digital archives of EarthRef.org where they

  13. 76 FR 1180 - FDA Transparency Initiative: Improving Transparency to Regulated Industry

    Science.gov (United States)

    2011-01-07

    ...] FDA Transparency Initiative: Improving Transparency to Regulated Industry AGENCY: Food and Drug... the Transparency Initiative, the Food and Drug Administration (FDA) is announcing the availability of a report entitled ``FDA Transparency Initiative: Improving Transparency to Regulated Industry.'' The...

  14. Online Patent Searching: The Realities.

    Science.gov (United States)

    Kaback, Stuart M.

    1983-01-01

    Considers patent subject searching capabilities of major online databases, noting patent claims, "deep-indexed" files, test searches, retrieval of related references, multi-database searching, improvements needed in indexing of chemical structures, full text searching, improvements needed in handling numerical data, and augmenting a…

  15. Citation searches are more sensitive than keyword searches to identify studies using specific measurement instruments.

    Science.gov (United States)

    Linder, Suzanne K; Kamath, Geetanjali R; Pratt, Gregory F; Saraykar, Smita S; Volk, Robert J

    2015-04-01

    To compare the effectiveness of two search methods in identifying studies that used the Control Preferences Scale (CPS), a health care decision-making instrument commonly used in clinical settings. We searched the literature using two methods: (1) keyword searching using variations of "Control Preferences Scale" and (2) cited reference searching using two seminal CPS publications. We searched three bibliographic databases [PubMed, Scopus, and Web of Science (WOS)] and one full-text database (Google Scholar). We report precision and sensitivity as measures of effectiveness. Keyword searches in bibliographic databases yielded high average precision (90%) but low average sensitivity (16%). PubMed was the most precise, followed closely by Scopus and WOS. The Google Scholar keyword search had low precision (54%) but provided the highest sensitivity (70%). Cited reference searches in all databases yielded moderate sensitivity (45-54%), but precision ranged from 35% to 75% with Scopus being the most precise. Cited reference searches were more sensitive than keyword searches, making it a more comprehensive strategy to identify all studies that use a particular instrument. Keyword searches provide a quick way of finding some but not all relevant articles. Goals, time, and resources should dictate the combination of which methods and databases are used. Copyright © 2015 Elsevier Inc. All rights reserved.

  16. 21 CFR 312.86 - Focused FDA regulatory research.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 5 2010-04-01 2010-04-01 false Focused FDA regulatory research. 312.86 Section 312.86 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED... Severely-debilitating Illnesses § 312.86 Focused FDA regulatory research. At the discretion of the agency...

  17. Usability Testing of a Large, Multidisciplinary Library Database: Basic Search and Visual Search

    Directory of Open Access Journals (Sweden)

    Jody Condit Fagan

    2006-09-01

    Full Text Available Visual search interfaces have been shown by researchers to assist users with information search and retrieval. Recently, several major library vendors have added visual search interfaces or functions to their products. For public service librarians, perhaps the most critical area of interest is the extent to which visual search interfaces and text-based search interfaces support research. This study presents the results of eight full-scale usability tests of both the EBSCOhost Basic Search and Visual Search in the context of a large liberal arts university.

  18. Update History of This Database - Q-TARO | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us Q-TARO Update History of This Database Date Update contents 2014/10/20 The URL of the portal...ption Download License Update History of This Database Site Policy | Contact Us Update History of This Database - Q-TARO | LSDB Archive ... ... site is changed. 2013/12/17 The URL of the portal site is changed. 2013/12/13 Q-TARO English archive site i...s opened. 2009/11/15 Q-TARO ( http://qtaro.abr.affrc.go.jp/ ) is opened. About This Database Database Descri

  19. The VirusBanker database uses a Java program to allow flexible searching through Bunyaviridae sequences

    Directory of Open Access Journals (Sweden)

    Gibbs Mark J

    2008-02-01

    Full Text Available Abstract Background Viruses of the Bunyaviridae have segmented negative-stranded RNA genomes and several of them cause significant disease. Many partial sequences have been obtained from the segments so that GenBank searches give complex results. Sequence databases usually use HTML pages to mediate remote sorting, but this approach can be limiting and may discourage a user from exploring a database. Results The VirusBanker database contains Bunyaviridae sequences and alignments and is presented as two spreadsheets generated by a Java program that interacts with a MySQL database on a server. Sequences are displayed in rows and may be sorted using information that is displayed in columns and includes data relating to the segment, gene, protein, species, strain, sequence length, terminal sequence and date and country of isolation. Bunyaviridae sequences and alignments may be downloaded from the second spreadsheet with titles defined by the user from the columns, or viewed when passed directly to the sequence editor, Jalview. Conclusion VirusBanker allows large datasets of aligned nucleotide and protein sequences from the Bunyaviridae to be compiled and winnowed rapidly using criteria that are formulated heuristically.

  20. Database searching and accounting of multiplexed precursor and product ion spectra from the data independent analysis of simple and complex peptide mixtures.

    Science.gov (United States)

    Li, Guo-Zhong; Vissers, Johannes P C; Silva, Jeffrey C; Golick, Dan; Gorenstein, Marc V; Geromanos, Scott J

    2009-03-01

    A novel database search algorithm is presented for the qualitative identification of proteins over a wide dynamic range, both in simple and complex biological samples. The algorithm has been designed for the analysis of data originating from data independent acquisitions, whereby multiple precursor ions are fragmented simultaneously. Measurements used by the algorithm include retention time, ion intensities, charge state, and accurate masses on both precursor and product ions from LC-MS data. The search algorithm uses an iterative process whereby each iteration incrementally increases the selectivity, specificity, and sensitivity of the overall strategy. Increased specificity is obtained by utilizing a subset database search approach, whereby for each subsequent stage of the search, only those peptides from securely identified proteins are queried. Tentative peptide and protein identifications are ranked and scored by their relative correlation to a number of models of known and empirically derived physicochemical attributes of proteins and peptides. In addition, the algorithm utilizes decoy database techniques for automatically determining the false positive identification rates. The search algorithm has been tested by comparing the search results from a four-protein mixture, the same four-protein mixture spiked into a complex biological background, and a variety of other "system" type protein digest mixtures. The method was validated independently by data dependent methods, while concurrently relying on replication and selectivity. Comparisons were also performed with other commercially and publicly available peptide fragmentation search algorithms. The presented results demonstrate the ability to correctly identify peptides and proteins from data independent acquisition strategies with high sensitivity and specificity. They also illustrate a more comprehensive analysis of the samples studied; providing approximately 20% more protein identifications, compared to

  1. JICST Factual DatabaseJICST Chemical Substance Safety Regulation Database

    Science.gov (United States)

    Abe, Atsushi; Sohma, Tohru

    JICST Chemical Substance Safety Regulation Database is based on the Database of Safety Laws for Chemical Compounds constructed by Japan Chemical Industry Ecology-Toxicology & Information Center (JETOC) sponsored by the Sience and Technology Agency in 1987. JICST has modified JETOC database system, added data and started the online service through JOlS-F (JICST Online Information Service-Factual database) in January 1990. JICST database comprises eighty-three laws and fourteen hundred compounds. The authors outline the database, data items, files and search commands. An example of online session is presented.

  2. Gottlieb, the FDA and dumbing down medicine

    OpenAIRE

    Robbins RA

    2017-01-01

    No abstract available. Article truncated at 150 words. In the last few weeks several events have occurred that might impact drug approval in the US. President Donald Trump's pick for FDA commissioner, Dr. Scott Gottlieb. Gottlieb, like many of Trump’s picks for administration healthcare positions, is a physician. He also has experience as deputy FDA commissioner from 2005-7. However, his confirmation hearing before the Senate Committee on Health, Education, Labor and Pensions alarmed some wh...

  3. RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures

    Directory of Open Access Journals (Sweden)

    Wasik Szymon

    2010-05-01

    Full Text Available Abstract Background Recent discoveries concerning novel functions of RNA, such as RNA interference, have contributed towards the growing importance of the field. In this respect, a deeper knowledge of complex three-dimensional RNA structures is essential to understand their new biological functions. A number of bioinformatic tools have been proposed to explore two major structural databases (PDB, NDB in order to analyze various aspects of RNA tertiary structures. One of these tools is RNA FRABASE 1.0, the first web-accessible database with an engine for automatic search of 3D fragments within PDB-derived RNA structures. This search is based upon the user-defined RNA secondary structure pattern. In this paper, we present and discuss RNA FRABASE 2.0. This second version of the system represents a major extension of this tool in terms of providing new data and a wide spectrum of novel functionalities. An intuitionally operated web server platform enables very fast user-tailored search of three-dimensional RNA fragments, their multi-parameter conformational analysis and visualization. Description RNA FRABASE 2.0 has stored information on 1565 PDB-deposited RNA structures, including all NMR models. The RNA FRABASE 2.0 search engine algorithms operate on the database of the RNA sequences and the new library of RNA secondary structures, coded in the dot-bracket format extended to hold multi-stranded structures and to cover residues whose coordinates are missing in the PDB files. The library of RNA secondary structures (and their graphics is made available. A high level of efficiency of the 3D search has been achieved by introducing novel tools to formulate advanced searching patterns and to screen highly populated tertiary structure elements. RNA FRABASE 2.0 also stores data and conformational parameters in order to provide "on the spot" structural filters to explore the three-dimensional RNA structures. An instant visualization of the 3D RNA

  4. Constructing Effective Search Strategies for Electronic Searching.

    Science.gov (United States)

    Flanagan, Lynn; Parente, Sharon Campbell

    Electronic databases have grown tremendously in both number and popularity since their development during the 1960s. Access to electronic databases in academic libraries was originally offered primarily through mediated search services by trained librarians; however, the advent of CD-ROM and end-user interfaces for online databases has shifted the…

  5. Constructing the informatics and information technology foundations of a medical device evaluation system: a report from the FDA unique device identifier demonstration.

    Science.gov (United States)

    Drozda, Joseph P; Roach, James; Forsyth, Thomas; Helmering, Paul; Dummitt, Benjamin; Tcheng, James E

    2018-02-01

    The US Food and Drug Administration (FDA) has recognized the need to improve the tracking of medical device safety and performance, with implementation of Unique Device Identifiers (UDIs) in electronic health information as a key strategy. The FDA funded a demonstration by Mercy Health wherein prototype UDIs were incorporated into its electronic information systems. This report describes the demonstration's informatics architecture. Prototype UDIs for coronary stents were created and implemented across a series of information systems, resulting in UDI-associated data flow from manufacture through point of use to long-term follow-up, with barcode scanning linking clinical data with UDI-associated device attributes. A reference database containing device attributes and the UDI Research and Surveillance Database (UDIR) containing the linked clinical and device information were created, enabling longitudinal assessment of device performance. The demonstration included many stakeholders: multiple Mercy departments, manufacturers, health system partners, the FDA, professional societies, the National Cardiovascular Data Registry, and information system vendors. The resulting system of systems is described in detail, including entities, functions, linkage between the UDIR and proprietary systems using UDIs as the index key, data flow, roles and responsibilities of actors, and the UDIR data model. The demonstration provided proof of concept that UDIs can be incorporated into provider and enterprise electronic information systems and used as the index key to combine device and clinical data in a database useful for device evaluation. Keys to success and challenges to achieving this goal were identified. Fundamental informatics principles were central to accomplishing the system of systems model. © The Author 2017. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  6. Database Dump - fRNAdb | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us fRNAdb Database Dump Data detail Data name Database Dump DOI 10.18908/lsdba.nbdc00452-002 De... data (tab separeted text) Data file File name: Database_Dump File URL: ftp://ftp....biosciencedbc.jp/archive/frnadb/LATEST/Database_Dump File size: 673 MB Simple search URL - Data acquisition...s. Data analysis method - Number of data entries 4 files - About This Database Database Description Download... License Update History of This Database Site Policy | Contact Us Database Dump - fRNAdb | LSDB Archive ...

  7. Gottlieb, the FDA and dumbing down medicine

    Directory of Open Access Journals (Sweden)

    Robbins RA

    2017-04-01

    Full Text Available No abstract available. Article truncated at 150 words. In the last few weeks several events have occurred that might impact drug approval in the US. President Donald Trump's pick for FDA commissioner, Dr. Scott Gottlieb. Gottlieb, like many of Trump’s picks for administration healthcare positions, is a physician. He also has experience as deputy FDA commissioner from 2005-7. However, his confirmation hearing before the Senate Committee on Health, Education, Labor and Pensions alarmed some who say his deep ties to the pharmaceutical industry will cause a conflict of interest (1. Others praised Gottlieb as the right man to lead the FDA. As opposed to Trump, Gottlieb denied any connection between vaccines and autism (1,2. Dr. Gottlieb called the issue "one of the most exhaustively studied questions in medical history," before saying, "There is no plausible link between vaccines and autism. At some point, we have to accept 'no' for an answer." However, Gottlieb did not give a straight …

  8. Seismic Search Engine: A distributed database for mining large scale seismic data

    Science.gov (United States)

    Liu, Y.; Vaidya, S.; Kuzma, H. A.

    2009-12-01

    The International Monitoring System (IMS) of the CTBTO collects terabytes worth of seismic measurements from many receiver stations situated around the earth with the goal of detecting underground nuclear testing events and distinguishing them from other benign, but more common events such as earthquakes and mine blasts. The International Data Center (IDC) processes and analyzes these measurements, as they are collected by the IMS, to summarize event detections in daily bulletins. Thereafter, the data measurements are archived into a large format database. Our proposed Seismic Search Engine (SSE) will facilitate a framework for data exploration of the seismic database as well as the development of seismic data mining algorithms. Analogous to GenBank, the annotated genetic sequence database maintained by NIH, through SSE, we intend to provide public access to seismic data and a set of processing and analysis tools, along with community-generated annotations and statistical models to help interpret the data. SSE will implement queries as user-defined functions composed from standard tools and models. Each query is compiled and executed over the database internally before reporting results back to the user. Since queries are expressed with standard tools and models, users can easily reproduce published results within this framework for peer-review and making metric comparisons. As an illustration, an example query is “what are the best receiver stations in East Asia for detecting events in the Middle East?” Evaluating this query involves listing all receiver stations in East Asia, characterizing known seismic events in that region, and constructing a profile for each receiver station to determine how effective its measurements are at predicting each event. The results of this query can be used to help prioritize how data is collected, identify defective instruments, and guide future sensor placements.

  9. 42 CFR 405.203 - FDA categorization of investigational devices.

    Science.gov (United States)

    2010-10-01

    ... 42 Public Health 2 2010-10-01 2010-10-01 false FDA categorization of investigational devices. 405... Coverage Decisions That Relate to Health Care Technology § 405.203 FDA categorization of investigational.../investigational (Category A) or non-experimental/investigational (Category B). (c) CMS uses the categorization of...

  10. Geroprotectors.org: a new, structured and curated database of current therapeutic interventions in aging and age-related disease

    Science.gov (United States)

    Moskalev, Alexey; Chernyagina, Elizaveta; de Magalhães, João Pedro; Barardo, Diogo; Thoppil, Harikrishnan; Shaposhnikov, Mikhail; Budovsky, Arie; Fraifeld, Vadim E.; Garazha, Andrew; Tsvetkov, Vasily; Bronovitsky, Evgeny; Bogomolov, Vladislav; Scerbacov, Alexei; Kuryan, Oleg; Gurinovich, Roman; Jellen, Leslie C.; Kennedy, Brian; Mamoshina, Polina; Dobrovolskaya, Evgeniya; Aliper, Alex; Kaminsky, Dmitry; Zhavoronkov, Alex

    2015-01-01

    As the level of interest in aging research increases, there is a growing number of geroprotectors, or therapeutic interventions that aim to extend the healthy lifespan and repair or reduce aging-related damage in model organisms and, eventually, in humans. There is a clear need for a manually-curated database of geroprotectors to compile and index their effects on aging and age-related diseases and link these effects to relevant studies and multiple biochemical and drug databases. Here, we introduce the first such resource, Geroprotectors (http://geroprotectors.org). Geroprotectors is a public, rapidly explorable database that catalogs over 250 experiments involving over 200 known or candidate geroprotectors that extend lifespan in model organisms. Each compound has a comprehensive profile complete with biochemistry, mechanisms, and lifespan effects in various model organisms, along with information ranging from chemical structure, side effects, and toxicity to FDA drug status. These are presented in a visually intuitive, efficient framework fit for casual browsing or in-depth research alike. Data are linked to the source studies or databases, providing quick and convenient access to original data. The Geroprotectors database facilitates cross-study, cross-organism, and cross-discipline analysis and saves countless hours of inefficient literature and web searching. Geroprotectors is a one-stop, knowledge-sharing, time-saving resource for researchers seeking healthy aging solutions. PMID:26342919

  11. Public Awareness of Uterine Power Morcellation Through US Food and Drug Administration Communications: Analysis of Google Trends Search Term Patterns.

    Science.gov (United States)

    Wood, Lauren N; Jamnagerwalla, Juzar; Markowitz, Melissa A; Thum, D Joseph; McCarty, Philip; Medendorp, Andrew R; Raz, Shlomo; Kim, Ja-Hong

    2018-04-26

    Uterine power morcellation, where the uterus is shred into smaller pieces, is a widely used technique for removal of uterine specimens in patients undergoing minimally invasive abdominal hysterectomy or myomectomy. Complications related to power morcellation of uterine specimens led to US Food and Drug Administration (FDA) communications in 2014 ultimately recommending against the use of power morcellation for women undergoing minimally invasive hysterectomy. Subsequently, practitioners drastically decreased the use of morcellation. We aimed to determine the effect of increased patient awareness on the decrease in use of the morcellator. Google Trends is a public tool that provides data on temporal patterns of search terms, and we correlated this data with the timing of the FDA communication. Weekly relative search volume (RSV) was obtained from Google Trends using the term “morcellation.” Higher RSV corresponds to increases in weekly search volume. Search volumes were divided into 3 groups: the 2 years prior to the FDA communication, a 1-year period following, and thereafter, with the distribution of the weekly RSV over the 3 periods tested using 1-way analysis of variance. Additionally, we analyzed the total number of websites containing the term “morcellation” over this time. The mean RSV prior to the FDA communication was 12.0 (SD 15.8), with the RSV being 60.3 (SD 24.7) in the 1-year after and 19.3 (SD 5.2) thereafter (PGoogle search activity about morcellation of uterine specimens increased significantly after the FDA communications. This trend indicates an increased public awareness regarding morcellation and its complications. More extensive preoperative counseling and alteration of surgical technique and clinician practice may be necessary. ©Lauren N Wood, Juzar Jamnagerwalla, Melissa A Markowitz, D Joseph Thum, Philip McCarty, Andrew R Medendorp, Shlomo Raz, Ja-Hong Kim. Originally published in JMIR Public Health and Surveillance (http

  12. A survey of the FDA's AERS database regarding muscle and tendon adverse events linked to the statin drug class.

    Directory of Open Access Journals (Sweden)

    Keith B Hoffman

    Full Text Available BACKGROUND: Cholesterol management drugs known as statins are widely used and often well tolerated; however, a variety of muscle-related side effects can arise. These adverse events (AEs can have serious impact, and form a significant barrier to therapy adherence. Surveillance of post-marketing AEs is of vital importance to understand real-world AEs and reporting differences between individual statin drugs. We conducted a review of post-approval muscle and tendon AE reports in association with statin use, to assess differences within the drug class. METHODS: We analyzed all case reports from the FDA AE Reporting System (AERS database linking muscle-related AEs to statin use (07/01/2005-03/31/2011. Drugs examined were: atorvastatin, simvastatin, lovastatin, pravastatin, rosuvastatin, and fluvastatin. RESULTS: Relative risk rates for rosuvastatin were consistently higher than other statins. Atorvastatin and simvastatin showed intermediate risks, while pravastatin and lovastatin appeared to have the lowest risk rates. Relative risk of muscle-related AEs, therefore, approximately tracked with per milligram LDL-lowering potency, with fluvastatin an apparent exception. Incorporating all muscle categories, rates for atorvastatin, simvastatin, pravastatin, and lovastatin were, respectively, 55%, 26%, 17%, and 7.5% as high, as rosuvastatin, approximately tracking per milligram potency (Rosuvastatin>Atorvastatin>Simvastatin>Pravastatin ≈ Lovastatin and comporting with findings of other studies. Relative potency, therefore, appears to be a fundamental predictor of muscle-related AE risk, with fluvastatin, the least potent statin, an apparent exception (risk 74% vs rosuvastatin. INTERPRETATION: AE reporting rates differed strikingly for drugs within the statin class, with relative reporting aligning substantially with potency. The data presented in this report offer important reference points for the selection of statins for cholesterol management in

  13. Searching the Literatura Latino Americana e do Caribe em Ciências da Saúde (LILACS) database improves systematic reviews.

    Science.gov (United States)

    Clark, Otavio Augusto Camara; Castro, Aldemar Araujo

    2002-02-01

    An unbiased systematic review (SR) should analyse as many articles as possible in order to provide the best evidence available. However, many SR use only databases with high English-language content as sources for articles. Literatura Latino Americana e do Caribe em Ciências da Saúde (LILACS) indexes 670 journals from the Latin American and Caribbean health literature but is seldom used in these SR. Our objective is to evaluate if LILACS should be used as a routine source of articles for SR. First we identified SR published in 1997 in five medical journals with a high impact factor. Then we searched LILACS for articles that could match the inclusion criteria of these SR. We also checked if the authors had already identified these articles located in LILACS. In all, 64 SR were identified. Two had already searched LILACS and were excluded. In 39 of 62 (63%) SR a LILACS search identified articles that matched the inclusion criteria. In 5 (8%) our search was inconclusive and in 18 (29%) no articles were found in LILACS. Therefore, in 71% (44/72) of cases, a LILACS search could have been useful to the authors. This proportion remains the same if we consider only the 37 SR that performed a meta-analysis. In only one case had the article identified in LILACS already been located elsewhere by the authors' strategy. LILACS is an under-explored and unique source of articles whose use can improve the quality of systematic reviews. This database should be used as a routine source to identify studies for systematic reviews.

  14. Update History of This Database - FANTOM5 | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available CAGE TSS aggregation 」 「 CAGE peaks 」 2015/12/07 FANTOM5 archive site is opened. (Archive V1) 2014/03/27 FANTOM5 ( http://fantom...switchLanguage; BLAST Search Image Search Home About Archive Update History Data List Contact us FANTOM...5 Update History of This Database Date Update contents 2017/03/14 FANTOM5 English arch...escription Download License Update History of This Database Site Policy | Contact Us Update History of This Database - FANTOM5 | LSDB Archive ...

  15. FDA drug safety communications: a narrative review and clinical considerations for older adults.

    Science.gov (United States)

    Marcum, Zachary A; Vande Griend, Joseph P; Linnebur, Sunny A

    2012-08-01

    The US Food and Drug Administration (FDA) has new regulatory authorities intended to enhance drug safety monitoring in the postmarketing period. This has resulted in an increase in communication from the FDA in recent years about the safety profile of certain drugs. It is important to stay abreast of the current literature on drug risks to effectively communicate these risks to patients, other health care providers, and the general public. To summarize 4 new FDA drug safety communications by describing the evidence supporting the risks and the clinical implications for older adults. The FDA Web site was reviewed for new drug safety communications from May 2011 to April 2012 that would be relevant to older adults. Approved labeling for each drug or class was obtained from the manufacturer, and PubMed was searched for primary literature that supported the drug safety concern. FDA drug safety communications for 4 drugs were chosen because of the potential clinical importance in older adults. A warning for citalopram was made because of potential problems with QT prolongation in patients taking less than 40 mg per day. The evidence suggests minor changes in QT interval. Given the flat dose-response curve in treating depression with citalopram, the new 20-mg/d maximum dose in older adults is sensible. Another warning was made for proton pump inhibitors (PPIs) and an increased risk of Clostridium difficile infection. A dose-response relationship was found for this drug risk. With C. difficile infections on the rise in older adults, along with other safety risks of PPI therapy, PPIs should only be used in older adults indicated for therapy for the shortest duration possible. In addition, a warning about dabigatran was made. There is strong evidence from a large clinical trial, as well as case reports, of increased bleeding risk in older adults taking dabigatran, especially in older adults with decreased renal function. This medication should be used with caution in older

  16. Healthy public relations: the FDA's 1930s legislative campaign.

    Science.gov (United States)

    Kay, G

    2001-01-01

    In this article, I argue that the Food and Drug Administration (FDA) is an oft-overlooked government agency that acts to preserve and secure the public's health. From its early years as an agency charged with enforcement of the 1906 Pure Food and Drugs Act, the FDA not only protected the public's health but also made the public aware of its mission, using methods as diverse as displays at county fairs and at the 1933 Chicago World's Fair, radio programming, and active correspondence. The agency encouraged the public to protect itself, particularly in those arenas in which the FDA had no regulatory authority. In addition, it may have overstepped its boundaries when it actively solicited public support for a bill submitted to Congress in the early 1930s. In the dark days of the Great Depression, the FDA contended not only with limited resources and its own feelings of inadequacy in terms of what could and could not be done to protect the populace, but also with "guinea pig" books that horrified and angered many readers. By 1938, when the agency prevailed and the revisions to the 1906 Act passed Congress and were signed into law by President Franklin D. Roosevelt, the FDA had done all that a responsible public health agency should do, and more.

  17. Acute renal failure with sodium-glucose-cotransporter-2 inhibitors: Analysis of the FDA adverse event report system database.

    Science.gov (United States)

    Perlman, A; Heyman, S N; Matok, I; Stokar, J; Muszkat, M; Szalat, A

    2017-12-01

    Sodium-glucose-cotransporter-2 (SGLT2) inhibitors have recently been approved for the treatment of type II diabetes mellitus (T2DM). It has been proposed that these agents could induce acute renal failure (ARF) under certain conditions. This study aimed to evaluate the association between SGLT2-inhibitors and ARF in the FDA adverse event report system (FAERS) database. We analyzed adverse event cases submitted to FAERS between January 2013 and September 2016. ARF cases were identified using a structured medical query. Medications were identified using both brand and generic names. During the period evaluated, 18,915 reports (out of a total of 3,832,015 registered in FAERS) involved the use of SGLT2-inhibitors. SGLT2-inhibitors were reportedly associated with ARF in 1224 of these cases (6.4%), and were defined as the "primary" or "secondary" cause of the adverse event in 96.8% of these cases. The proportion of reports with ARF among reports with SGLT2 inhibitor was almost three-fold higher compared to reports without these drugs (ROR 2.88, 95% CI 2.71-3.05, p SGLT2-inhibitors was significantly greater than the proportion of ARF among cases with T2DM without SGLT2-inhibitors (ROR 1.68, 95% CI 1.57-1.8, p SGLT2-inhibitors, canagliflozin was associated with a higher proportion of reports of renal failure (7.3%), compared to empagliflozin and dapagliflozin (4.7% and 4.8% respectively, p SGLT2-inhibitors are associated with an increase in the proportion of reports of ARF compared to other medications. SGLT2-inhibitor agents may differ from one another in their respective risk for ARF. Copyright © 2017 The Italian Society of Diabetology, the Italian Society for the Study of Atherosclerosis, the Italian Society of Human Nutrition, and the Department of Clinical Medicine and Surgery, Federico II University. Published by Elsevier B.V. All rights reserved.

  18. Usability of some databases for information services in Czechoslovak nuclear programme

    International Nuclear Information System (INIS)

    Kakos, A.

    1988-01-01

    The contents were compared of the databases Chemical Abstracts Search, World Patent Index, Excerpta Medica, Inspec and Compendex with INIS, with regard to possible completing of INIS searches with searches in these other databases. On the basis of the results of test searches made in all said databases on selected topics falling under the INIS scope, concrete cases were determined when INIS searches should be completed with data in some of the other databases. The contents analysis method is described with regard to the concrete search topics and areas are given of the overlapping of the databases with INIS. Numerical results are given. (J.B.). 2 tabs

  19. Drug disposition and drug-drug interaction data in 2013 FDA new drug applications: a systematic review.

    Science.gov (United States)

    Yu, Jingjing; Ritchie, Tasha K; Mulgaonkar, Aditi; Ragueneau-Majlessi, Isabelle

    2014-12-01

    The aim of the present work was to perform a systematic review of drug metabolism, transport, pharmacokinetics, and DDI data available in the NDAs approved by the FDA in 2013, using the University of Washington Drug Interaction Database, and to highlight significant findings. Among 27 NMEs approved, 22 (81%) were well characterized with regard to drug metabolism, transport, or organ impairment, in accordance with the FDA drug interaction guidance (2012) and were fully analyzed in this review. In vitro, a majority of the NMEs were found to be substrates or inhibitors/inducers of at least one drug metabolizing enzyme or transporter. However, in vivo, only half (n = 11) showed clinically relevant drug interactions, with most related to the NMEs as victim drugs and CYP3A being the most affected enzyme. As perpetrators, the overall effects for NMEs were much less pronounced, compared with when they served as victims. In addition, the pharmacokinetic evaluation in patients with hepatic or renal impairment provided useful information for further understanding of the drugs' disposition. Copyright © 2014 by The American Society for Pharmacology and Experimental Therapeutics.

  20. CUDASW++2.0: enhanced Smith-Waterman protein database search on CUDA-enabled GPUs based on SIMT and virtualized SIMD abstractions

    Directory of Open Access Journals (Sweden)

    Schmidt Bertil

    2010-04-01

    Full Text Available Abstract Background Due to its high sensitivity, the Smith-Waterman algorithm is widely used for biological database searches. Unfortunately, the quadratic time complexity of this algorithm makes it highly time-consuming. The exponential growth of biological databases further deteriorates the situation. To accelerate this algorithm, many efforts have been made to develop techniques in high performance architectures, especially the recently emerging many-core architectures and their associated programming models. Findings This paper describes the latest release of the CUDASW++ software, CUDASW++ 2.0, which makes new contributions to Smith-Waterman protein database searches using compute unified device architecture (CUDA. A parallel Smith-Waterman algorithm is proposed to further optimize the performance of CUDASW++ 1.0 based on the single instruction, multiple thread (SIMT abstraction. For the first time, we have investigated a partitioned vectorized Smith-Waterman algorithm using CUDA based on the virtualized single instruction, multiple data (SIMD abstraction. The optimized SIMT and the partitioned vectorized algorithms were benchmarked, and remarkably, have similar performance characteristics. CUDASW++ 2.0 achieves performance improvement over CUDASW++ 1.0 as much as 1.74 (1.72 times using the optimized SIMT algorithm and up to 1.77 (1.66 times using the partitioned vectorized algorithm, with a performance of up to 17 (30 billion cells update per second (GCUPS on a single-GPU GeForce GTX 280 (dual-GPU GeForce GTX 295 graphics card. Conclusions CUDASW++ 2.0 is publicly available open-source software, written in CUDA and C++ programming languages. It obtains significant performance improvement over CUDASW++ 1.0 using either the optimized SIMT algorithm or the partitioned vectorized algorithm for Smith-Waterman protein database searches by fully exploiting the compute capability of commonly used CUDA-enabled low-cost GPUs.

  1. Alignment - SAHG | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...e URL: ftp://ftp.biosciencedbc.jp/archive/sahg/LATEST/sahg_alignment.zip File size: 12.0 MB Simple search UR...s Database Database Description Download License Update History of This Database Site Policy | Contact Us Alignment - SAHG | LSDB Archive ...

  2. Locus - ASTRA | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...URL: ftp://ftp.biosciencedbc.jp/archive/astra/LATEST/astra_locus.zip File size: 887 KB Simple search URL htt...icing type (ex. cassette) About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Locus - ASTRA | LSDB Archive ...

  3. License - JSNP | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...This Database Database Description Download License Update History of This Database Site Policy | Contact Us License - JSNP | LSDB Archive ...

  4. Download - ASTRA | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...is Database Database Description Download License Update History of This Database Site Policy | Contact Us Download - ASTRA | LSDB Archive ...

  5. License - KOME | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...out This Database Database Description Download License Update History of This Database Site Policy | Contact Us License - KOME | LSDB Archive ...

  6. Download - RED | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...t This Database Database Description Download License Update History of This Database Site Policy | Contact Us Download - RED | LSDB Archive ...

  7. Download - GRIPDB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...t This Database Database Description Download License Update History of This Database Site Policy | Contact Us Download - GRIPDB | LSDB Archive ...

  8. License - RMOS | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...out This Database Database Description Download License Update History of This Database Site Policy | Contact Us License - RMOS | LSDB Archive ...

  9. The Open Spectral Database: an open platform for sharing and searching spectral data.

    Science.gov (United States)

    Chalk, Stuart J

    2016-01-01

    A number of websites make available spectral data for download (typically as JCAMP-DX text files) and one (ChemSpider) that also allows users to contribute spectral files. As a result, searching and retrieving such spectral data can be time consuming, and difficult to reuse if the data is compressed in the JCAMP-DX file. What is needed is a single resource that allows submission of JCAMP-DX files, export of the raw data in multiple formats, searching based on multiple chemical identifiers, and is open in terms of license and access. To address these issues a new online resource called the Open Spectral Database (OSDB) http://osdb.info/ has been developed and is now available. Built using open source tools, using open code (hosted on GitHub), providing open data, and open to community input about design and functionality, the OSDB is available for anyone to submit spectral data, making it searchable and available to the scientific community. This paper details the concept and coding, internal architecture, export formats, Representational State Transfer (REST) Application Programming Interface and options for submission of data. The OSDB website went live in November 2015. Concurrently, the GitHub repository was made available at https://github.com/stuchalk/OSDB/, and is open for collaborators to join the project, submit issues, and contribute code. The combination of a scripting environment (PHPStorm), a PHP Framework (CakePHP), a relational database (MySQL) and a code repository (GitHub) provides all the capabilities to easily develop REST based websites for ingestion, curation and exposure of open chemical data to the community at all levels. It is hoped this software stack (or equivalent ones in other scripting languages) will be leveraged to make more chemical data available for both humans and computers.

  10. Millennial Students’ Online Search Strategies are Associated With Their Mental Models of Search. A Review of: Holman, L. (2011. Millennial students’ mental models of search: Implications for academic librarians and database developers. Journal of Academic Librarianship, 37(1, 19-27. doi:10.1016/j.acalib.2010.10.003

    Directory of Open Access Journals (Sweden)

    Leslie Bussert

    2011-09-01

    Full Text Available Objective – To examine first-year college students’ information seeking behaviours and determine whether their mental models of the search process influence their ability to effectively search for and find scholarly materials.Design – Mixed methods including contextual inquiry, concept mapping, observation, and interviews.Setting – University of Baltimore, a public institution in Maryland, United States of America, offering undergraduate, graduate, and professional degrees.Subjects – A total of 21 first-year undergraduate students, ages 16 to 19 years, undertaking research assignments for which they chose to use online resources.Methods – First-year students were recruited in the fall of 2008 and met with the researcher in a university usability lab for about one hour over a three week period. The researcher observed and videotaped the students as they conducted research in their chosen search engines or article databases. The searches were captured using software, and students were encouraged to think aloud about their research process, search strategies, and anticipated search results. Observation sessions concluded with a 10-question interview incorporating a review of the keywords the student used, the student’s reflection on the success of his or her searches, and possible alternate keywords. The interview also offered prompts to help the researcher learn about students’ conceptualizations of search tools’ utilization of keywords to generate results. The researcher then asked the students to provide a visual diagram of the relationship between their search terms and the items retrieved in the search tool.Data were analyzed by identifying the 21 different search tools used by the students and categorizing all 210 searches and student diagrams for further analysis. A scheme similar to Guinee, Eagleton, and Hall’s (2003 characterized the student searches into four categories: simple single-term searches, topic plus focus

  11. License - ASTRA | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ... notice. About This Database Database Description Download License Update History of This Database Site Policy | Contact Us License - ASTRA | LSDB Archive ...

  12. License - SSBD | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...thout notice. About This Database Database Description Download License Update History of This Database Site Policy | Contact Us License - SSBD | LSDB Archive ...

  13. Download - PSCDB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...cess [here]. About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Download - PSCDB | LSDB Archive ...

  14. License - SAHG | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...ut notice. About This Database Database Description Download License Update History of This Database Site Policy | Contact Us License - SAHG | LSDB Archive ...

  15. License - RPSD | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...thout notice. About This Database Database Description Download License Update History of This Database Site Policy | Contact Us License - RPSD | LSDB Archive ...

  16. Subject search study. Final report

    International Nuclear Information System (INIS)

    Todeschini, C.

    1995-01-01

    The study gathered information on how users search the database of the International Nuclear Information System (INIS), using indicators such as Subject categories, Controlled terms, Subject headings, Free-text words, combinations of the above. Users participated from the Australian, French, Russian and Spanish INIS Centres, that have different national languages. Participants, both intermediaries and end users, replied to a questionnaire and executed search queries. The INIS Secretariat at the IAEA also participated. A protocol of all search strategies used in actual searches in the database was kept. The thought process for Russian and Spanish users is predominantly non-English and also the actual initial search formulation is predominantly non-English among Russian and Spanish users while it tends to be more in English among French users. A total of 1002 searches were executed by the five INIS centres including the IAEA. The search protocols indicate the following search behaviour: 1) free text words represent about 40% of search points on an average query; 2) descriptors used as search keys have the widest range as percentage of search points, from a low of 25% to a high of 48%; 3) search keys consisting of free text that coincides with a descriptor account for about 15% of search points; 4) Subject Categories are not used in many searches; 5) free text words are present as search points in about 80% of all searches; 6) controlled terms (descriptors) are used very extensively and appear in about 90% of all searches; 7) Subject Headings were used in only a few percent of searches. From the results of the study one can conclude that there is a greater reluctance on the part of non-native English speakers in initiating their searches by using free text word searches. Also: Subject Categories are little used in searching the database; both free text terms and controlled terms are the predominant types of search keys used, whereby the controlled terms are used more

  17. Download - RPD | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data .... If it is, access [here]. About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Download - RPD | LSDB Archive ...

  18. License - RED | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...ts might be changed without notice. About This Database Database Description Download License Update History of This Database Site Policy | Contact Us License - RED | LSDB Archive ...

  19. Download - JSNP | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data .... If it is, access [here]. About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Download - JSNP | LSDB Archive ...

  20. Trouble Spots in Online Direct-to-Consumer Prescription Drug Promotion: A Content Analysis of FDA Warning Letters.

    Science.gov (United States)

    Kim, Hyosun

    2015-08-25

    For the purpose of understanding the Food and Drug Administration's (FDA's) concerns regarding online promotion of prescription drugs advertised directly to consumers, this study examines notices of violations (NOVs) and warning letters issued by the FDA to pharmaceutical manufacturers. The FDA's warning letters and NOVs, which were issued to pharmaceutical companies over a 10-year period (2005 to 2014) regarding online promotional activities, were content-analyzed. Six violation categories were identified: risk information, efficacy information, indication information, product labeling, material information issues, and approval issues. The results reveal that approximately 95% of the alleged violations were found on branded drug websites, in online paid advertisements, and in online videos. Of the total 179 violations, the majority of the alleged violations were concerned with the lack of risk information and/or misrepresentation of efficacy information, suggesting that achieving a fair balance of benefit versus risk information is a major problem with regard to the direct-to-consumer advertising (DTCA) of prescription drugs. In addition, the character space limitations of online platforms, eg, sponsored links on search engines, pose challenges for pharmaceutical marketers with regard to adequately communicating important drug information, such as indication information, risk information, and product labeling. Presenting drug information in a fair and balanced manner remains a major problem. Industry guidance should consider addressing visibility and accessibility of information in the web environment to help pharmaceutical marketers meet the requirements for direct-to-consumer promotion and to protect consumers from misleading drug information. Promotion via social media warrants further attention, as pharmaceutical manufacturers have already begun actively establishing a social media presence, and the FDA has thus begun to keep tabs on social media promotions of

  1. Abstract databases in nuclear medicine; New database for articles not indexed in PubMed

    International Nuclear Information System (INIS)

    Ugrinska, A.; Mustafa, B.

    2004-01-01

    Full text: Abstract databases available on Internet free of charge were searched for nuclear medicine contents. The only comprehensive database found was PubMed. Analysis of nuclear medicine journals included in PubMed was performed. PubMed contains 25 medical journals that contain the phrase 'nuclear medicine' in different languages in their title. Searching the Internet with the search engine 'Google' we have found four more peer-reviewed journals with the phrase 'nuclear medicine' in their title. In addition, we are fully aware that many articles related to nuclear medicine are published in national medical journals devoted to general medicine. For example in year 2000 colleagues from Institute of Pathophysiology and Nuclear Medicine, Skopje, Macedonia have published 10 articles out of which none could be found on PubMed. This suggested that a big amount of research work is not accessible for the people professionally involved in nuclear medicine. Therefore, we have created a database framework for abstracts that couldn't be found in PubMed. The database is organized in user-friendly manner. There are two main sections: 'post an abstract' and 'search for abstracts'. Authors of the articles are expected to submit their work in the section 'post an abstract'. During the submission process authors should fill the separate boxes with the Title in English, Title in original language, Country of origin, Journal name, Volume, Issue and Pages. Authors should choose up to five keywords from a drop-down menu. Authors are encouraged if the abstract is not published in English to translate it. The section 'search for abstract' is searchable according to Author, Keywords, and words and phrases incorporated in the English title. The abstract database currently resides on an MS Access back-end, with a front-end in ASP (Active Server Pages). In the future, we plan to migrate the database on a MS SQL Server, which should provide a faster and more reliable framework for hosting a

  2. Hypersensitivity reactions to anticancer agents: Data mining of the public version of the FDA adverse event reporting system, AERS

    Directory of Open Access Journals (Sweden)

    Sakaeda Toshiyuki

    2011-10-01

    Full Text Available Abstract Background Previously, adverse event reports (AERs submitted to the US Food and Drug Administration (FDA database were reviewed to confirm platinum agent-associated hypersensitivity reactions. The present study was performed to confirm whether the database could suggest the hypersensitivity reactions caused by anticancer agents, paclitaxel, docetaxel, procarbazine, asparaginase, teniposide, and etoposide. Methods After a revision of arbitrary drug names and the deletion of duplicated submissions, AERs involving candidate agents were analyzed. The National Cancer Institute Common Terminology Criteria for Adverse Events version 4.0 was applied to evaluate the susceptibility to hypersensitivity reactions, and standardized official pharmacovigilance tools were used for quantitative detection of signals, i.e., drug-associated adverse events, including the proportional reporting ratio, the reporting odds ratio, the information component given by a Bayesian confidence propagation neural network, and the empirical Bayes geometric mean. Results Based on 1,644,220 AERs from 2004 to 2009, the signals were detected for paclitaxel-associated mild, severe, and lethal hypersensitivity reactions, and docetaxel-associated lethal reactions. However, the total number of adverse events occurring with procarbazine, asparaginase, teniposide, or etoposide was not large enough to detect signals. Conclusions The FDA's adverse event reporting system, AERS, and the data mining methods used herein are useful for confirming drug-associated adverse events, but the number of co-occurrences is an important factor in signal detection.

  3. NIST/Sandia/ICDD Electron Diffraction Database: A Database for Phase Identification by Electron Diffraction.

    Science.gov (United States)

    Carr, M J; Chambers, W F; Melgaard, D; Himes, V L; Stalick, J K; Mighell, A D

    1989-01-01

    A new database containing crystallographic and chemical information designed especially for application to electron diffraction search/match and related problems has been developed. The new database was derived from two well-established x-ray diffraction databases, the JCPDS Powder Diffraction File and NBS CRYSTAL DATA, and incorporates 2 years of experience with an earlier version. It contains 71,142 entries, with space group and unit cell data for 59,612 of those. Unit cell and space group information were used, where available, to calculate patterns consisting of all allowed reflections with d -spacings greater than 0.8 A for ~ 59,000 of the entries. Calculated patterns are used in the database in preference to experimental x-ray data when both are available, since experimental x-ray data sometimes omits high d -spacing data which falls at low diffraction angles. Intensity data are not given when calculated spacings are used. A search scheme using chemistry and r -spacing (reciprocal d -spacing) has been developed. Other potentially searchable data in this new database include space group, Pearson symbol, unit cell edge lengths, reduced cell edge length, and reduced cell volume. Compound and/or mineral names, formulas, and journal references are included in the output, as well as pointers to corresponding entries in NBS CRYSTAL DATA and the Powder Diffraction File where more complete information may be obtained. Atom positions are not given. Rudimentary search software has been written to implement a chemistry and r -spacing bit map search. With typical data, a full search through ~ 71,000 compounds takes 10~20 seconds on a PDP 11/23-RL02 system.

  4. Update History of This Database - tRNADB-CE | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data List Contact us tRNAD...11/08/25 License is updated. 2010/03/29 tRNADB-CE English archive site is opened. 2008/7/1 tRNADB-CE( http:/...Download License Update History of This Database Site Policy | Contact Us Update History of This Database - tRNADB-CE | LSDB Archive ...

  5. FDA Approves First Therapeutic Cancer Vaccine

    Science.gov (United States)

    Sipuleucel-T (Provenge) is a relatively nontoxic treatment option for men with hormone-resistant or castration-resistant prostate cancer. The FDA's approval of the vaccine represented the first proof of principle that immunotherapy can work in cancer.

  6. Main data - RMG | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...ftp://ftp.biosciencedbc.jp/archive/rmg/LATEST/rmg_main.zip File size: 1 KB Simple search URL http://togodb.b... This Database Database Description Download License Update History of This Database Site Policy | Contact Us Main data - RMG | LSDB Archive ...

  7. Complementary Value of Databases for Discovery of Scholarly Literature: A User Survey of Online Searching for Publications in Art History

    Science.gov (United States)

    Nemeth, Erik

    2010-01-01

    Discovery of academic literature through Web search engines challenges the traditional role of specialized research databases. Creation of literature outside academic presses and peer-reviewed publications expands the content for scholarly research within a particular field. The resulting body of literature raises the question of whether scholars…

  8. Predicting Drug Recalls From Internet Search Engine Queries.

    Science.gov (United States)

    Yom-Tov, Elad

    2017-01-01

    Batches of pharmaceuticals are sometimes recalled from the market when a safety issue or a defect is detected in specific production runs of a drug. Such problems are usually detected when patients or healthcare providers report abnormalities to medical authorities. Here, we test the hypothesis that defective production lots can be detected earlier by monitoring queries to Internet search engines. We extracted queries from the USA to the Bing search engine, which mentioned one of the 5195 pharmaceutical drugs during 2015 and all recall notifications issued by the Food and Drug Administration (FDA) during that year. By using attributes that quantify the change in query volume at the state level, we attempted to predict if a recall of a specific drug will be ordered by FDA in a time horizon ranging from 1 to 40 days in future. Our results show that future drug recalls can indeed be identified with an AUC of 0.791 and a lift at 5% of approximately 6 when predicting a recall occurring one day ahead. This performance degrades as prediction is made for longer periods ahead. The most indicative attributes for prediction are sudden spikes in query volume about a specific medicine in each state. Recalls of prescription drugs and those estimated to be of medium-risk are more likely to be identified using search query data. These findings suggest that aggregated Internet search engine data can be used to facilitate in early warning of faulty batches of medicines.

  9. Environmental assessments and findings of no significant impact--FDA. Notice.

    Science.gov (United States)

    1998-05-18

    The Food and Drug Administration (FDA) is announcing that it has reviewed environmental assessments (EA's) and issued findings of no significant impact (FONSI's) relating to the 167 new drug applications (NDA's) and supplemental applications listed in this document. FDA is publishing this notice because Federal regulations require public notice of the availability of environmental documents.

  10. 21 CFR 516.34 - FDA recognition of exclusive marketing rights.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 6 2010-04-01 2010-04-01 false FDA recognition of exclusive marketing rights. 516... SERVICES (CONTINUED) ANIMAL DRUGS, FEEDS, AND RELATED PRODUCTS NEW ANIMAL DRUGS FOR MINOR USE AND MINOR SPECIES Designation of a Minor Use or Minor Species New Animal Drug § 516.34 FDA recognition of exclusive...

  11. The Weaknesses of Full-Text Searching

    Science.gov (United States)

    Beall, Jeffrey

    2008-01-01

    This paper provides a theoretical critique of the deficiencies of full-text searching in academic library databases. Because full-text searching relies on matching words in a search query with words in online resources, it is an inefficient method of finding information in a database. This matching fails to retrieve synonyms, and it also retrieves…

  12. A comparison of three design tree based search algorithms for the detection of engineering parts constructed with CATIA V5 in large databases

    Directory of Open Access Journals (Sweden)

    Robin Roj

    2014-07-01

    Full Text Available This paper presents three different search engines for the detection of CAD-parts in large databases. The analysis of the contained information is performed by the export of the data that is stored in the structure trees of the CAD-models. A preparation program generates one XML-file for every model, which in addition to including the data of the structure tree, also owns certain physical properties of each part. The first search engine is specializes in the discovery of standard parts, like screws or washers. The second program uses certain user input as search parameters, and therefore has the ability to perform personalized queries. The third one compares one given reference part with all parts in the database, and locates files that are identical, or similar to, the reference part. All approaches run automatically, and have the analysis of the structure tree in common. Files constructed with CATIA V5, and search engines written with Python have been used for the implementation. The paper also includes a short comparison of the advantages and disadvantages of each program, as well as a performance test.

  13. The Impact of Online Bibliographic Databases on Teaching and Research in Political Science.

    Science.gov (United States)

    Reichel, Mary

    The availability of online bibliographic databases greatly facilitates literature searching in political science. The advantages to searching databases online include combination of concepts, comprehensiveness, multiple database searching, free-text searching, currency, current awareness services, document delivery service, and convenience.…

  14. E-MSD: the European Bioinformatics Institute Macromolecular Structure Database.

    Science.gov (United States)

    Boutselakis, H; Dimitropoulos, D; Fillon, J; Golovin, A; Henrick, K; Hussain, A; Ionides, J; John, M; Keller, P A; Krissinel, E; McNeil, P; Naim, A; Newman, R; Oldfield, T; Pineda, J; Rachedi, A; Copeland, J; Sitnov, A; Sobhany, S; Suarez-Uruena, A; Swaminathan, J; Tagari, M; Tate, J; Tromm, S; Velankar, S; Vranken, W

    2003-01-01

    The E-MSD macromolecular structure relational database (http://www.ebi.ac.uk/msd) is designed to be a single access point for protein and nucleic acid structures and related information. The database is derived from Protein Data Bank (PDB) entries. Relational database technologies are used in a comprehensive cleaning procedure to ensure data uniformity across the whole archive. The search database contains an extensive set of derived properties, goodness-of-fit indicators, and links to other EBI databases including InterPro, GO, and SWISS-PROT, together with links to SCOP, CATH, PFAM and PROSITE. A generic search interface is available, coupled with a fast secondary structure domain search tool.

  15. Formation of defect-free 6FDA-DAM asymmetric hollow fiber membranes for gas separations

    KAUST Repository

    Xu, Liren; Zhang, Chen; Rungta, Meha; Qiu, Wulin; Liu, Junqiang; Koros, William J.

    2014-01-01

    This paper reports the formation of defect-free 6FDA-DAM asymmetric hollow fiber membranes. 6FDA-polyimides are of great interest for advanced gas separation membranes, and 6FDA-DAM polyimide is a representative polymer in this family

  16. Gas separation performance of 6FDA-based polyimides with different chemical structures

    KAUST Repository

    Qiu, Wulin

    2013-10-01

    This work reports the gas separation performance of several 6FDA-based polyimides with different chemical structures, to correlate chemical structure with gas transport properties with a special focus on CO2 and CH 4 transport and plasticization stability of the polyimides membranes relevant to natural gas purification. The consideration of the other gases (He, O2 and N2) provided additional insights regarding effects of backbone structure on detailed penetrant properties. The polyimides studied include 6FDA-DAM, 6FDA-mPDA, 6FDA-DABA, 6FDA-DAM:DABA (3:2), 6FDA-DAM:mPDA (3:2) and 6FDA-mPDA:DABA (3:2). Both pure and binary gas permeation were investigated. The packing density, which is tunable by adjusting monomer type and composition of the various samples, correlated with transport permeability and selectivity. The separation performance of the polyimides for various gas pairs were also plotted for comparison to the upper bound curves, and it was found that this family of materials shows attractive performance. The CO 2 plasticization responses for the un-cross-linked polyimides showed good plasticization resistance to CO2/CH4 mixed gas with 10% CO2; however, only the cross-linked polyimides showed good plasticization resistance under aggressive gas feed conditions (CO 2/CH4 mixed gas with 50% CO2 or pure CO 2). For future work, asymmetric hollow fibers and carbon molecular sieve membranes based on the most attractive members of the family will be considered. © 2013 Elsevier Ltd. All rights reserved.

  17. Searching the PASCAL database - A user's perspective

    Science.gov (United States)

    Jack, Robert F.

    1989-01-01

    The operation of PASCAL, a bibliographic data base covering broad subject areas in science and technology, is discussed. The data base includes information from about 1973 to the present, including topics in engineering, chemistry, physics, earth science, environmental science, biology, psychology, and medicine. Data from 1986 to the present may be searched using DIALOG. The procedures and classification codes for searching PASCAL are presented. Examples of citations retrieved from the data base are given and suggestions are made concerning when to use PASCAL.

  18. The MAR databases: development and implementation of databases specific for marine metagenomics.

    Science.gov (United States)

    Klemetsen, Terje; Raknes, Inge A; Fu, Juan; Agafonov, Alexander; Balasundaram, Sudhagar V; Tartari, Giacomo; Robertsen, Espen; Willassen, Nils P

    2018-01-04

    We introduce the marine databases; MarRef, MarDB and MarCat (https://mmp.sfb.uit.no/databases/), which are publicly available resources that promote marine research and innovation. These data resources, which have been implemented in the Marine Metagenomics Portal (MMP) (https://mmp.sfb.uit.no/), are collections of richly annotated and manually curated contextual (metadata) and sequence databases representing three tiers of accuracy. While MarRef is a database for completely sequenced marine prokaryotic genomes, which represent a marine prokaryote reference genome database, MarDB includes all incomplete sequenced prokaryotic genomes regardless level of completeness. The last database, MarCat, represents a gene (protein) catalog of uncultivable (and cultivable) marine genes and proteins derived from marine metagenomics samples. The first versions of MarRef and MarDB contain 612 and 3726 records, respectively. Each record is built up of 106 metadata fields including attributes for sampling, sequencing, assembly and annotation in addition to the organism and taxonomic information. Currently, MarCat contains 1227 records with 55 metadata fields. Ontologies and controlled vocabularies are used in the contextual databases to enhance consistency. The user-friendly web interface lets the visitors browse, filter and search in the contextual databases and perform BLAST searches against the corresponding sequence databases. All contextual and sequence databases are freely accessible and downloadable from https://s1.sfb.uit.no/public/mar/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  19. NIMS structural materials databases and cross search engine - MatNavi

    Energy Technology Data Exchange (ETDEWEB)

    Yamazaki, M.; Xu, Y.; Murata, M.; Tanaka, H.; Kamihira, K.; Kimura, K. [National Institute for Materials Science, Tokyo (Japan)

    2007-06-15

    Materials Database Station (MDBS) of National Institute for Materials Science (NIMS) owns the world's largest Internet materials database for academic and industry purpose, which is composed of twelve databases: five concerning structural materials, five concerning basic physical properties, one for superconducting materials and one for polymers. All of theses databases are opened to Internet access at the website of http://mits.nims.go.jp/en. Online tools for predicting properties of polymers and composite materials are also available. The NIMS structural materials databases are composed of structural materials data sheet online version (creep, fatigue, corrosion and space use materials strength), microstructure for crept material database, Pressure vessel materials database and CCT diagram for welding. (orig.)

  20. License - Q-TARO | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...thout notice. About This Database Database Description Download License Update History of This Database Site Policy | Contact Us License - Q-TARO | LSDB Archive ...

  1. Download - GenLibi | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...access [here]. About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Download - GenLibi | LSDB Archive ...

  2. Automatic sorting of toxicological information into the IUCLID (International Uniform Chemical Information Database) endpoint-categories making use of the semantic search engine Go3R.

    Science.gov (United States)

    Sauer, Ursula G; Wächter, Thomas; Hareng, Lars; Wareing, Britta; Langsch, Angelika; Zschunke, Matthias; Alvers, Michael R; Landsiedel, Robert

    2014-06-01

    The knowledge-based search engine Go3R, www.Go3R.org, has been developed to assist scientists from industry and regulatory authorities in collecting comprehensive toxicological information with a special focus on identifying available alternatives to animal testing. The semantic search paradigm of Go3R makes use of expert knowledge on 3Rs methods and regulatory toxicology, laid down in the ontology, a network of concepts, terms, and synonyms, to recognize the contents of documents. Search results are automatically sorted into a dynamic table of contents presented alongside the list of documents retrieved. This table of contents allows the user to quickly filter the set of documents by topics of interest. Documents containing hazard information are automatically assigned to a user interface following the endpoint-specific IUCLID5 categorization scheme required, e.g. for REACH registration dossiers. For this purpose, complex endpoint-specific search queries were compiled and integrated into the search engine (based upon a gold standard of 310 references that had been assigned manually to the different endpoint categories). Go3R sorts 87% of the references concordantly into the respective IUCLID5 categories. Currently, Go3R searches in the 22 million documents available in the PubMed and TOXNET databases. However, it can be customized to search in other databases including in-house databanks. Copyright © 2013 Elsevier Ltd. All rights reserved.

  3. Formation of defect-free 6FDA-DAM asymmetric hollow fiber membranes for gas separations

    KAUST Repository

    Xu, Liren

    2014-06-01

    This paper reports the formation of defect-free 6FDA-DAM asymmetric hollow fiber membranes. 6FDA-polyimides are of great interest for advanced gas separation membranes, and 6FDA-DAM polyimide is a representative polymer in this family with attractive dense film properties for several potential applications. The work reported here for the 6FDA-DAM polyimide provides insight for the challenging fabrication of defect-free asymmetric hollow fiber membranes for this class of 6FDA-polyimides, which behave rather different from lower free volume polymers. Specifically, the 6FDA based materials show relatively slow phase separation rate in water quench baths, which presents a challenge for fiber spinning. For convenience, we refer to the behavior as more "non-solvent resistant" in comparison to other lower free volume polymers, since the binodal phase boundary is displaced further from the conventional position near the pure polymer-solvent axis on a ternary phase diagram in conventional polymers like Matrimid® and Ultem®. The addition of lithium nitrate to promote phase separation has a useful impact on 6FDA-DAM asymmetric hollow fiber formation. 6FDA-DAM phase diagrams using ethanol and water as non-solvent are reported, and it was found that water is less desirable as a non-solvent dope additive for defect-free fiber spinning. Phase diagrams are also reported for 6FDA-DAM dope formulation with and without the addition of lithium nitrate, and defect-free asymmetric hollow fiber membranes are reported for both cases. The effect of polymer molecular weight on defect-free fiber spinning was also investigated. Gas transport properties and morphology of hollow fibers were characterized. With several thorough case studies, this work provides a systematic guideline for defect-free fiber formation from 6FDA-polymers. © 2014 Elsevier B.V.

  4. LSDB Archive - KEGG MEDICUS | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] English ]; } else if ( url.search(//en//) != -1 ) { url = url.replace(/...switchLanguage; BLAST Search Image Search Home About Archive Update History Data List Contact us KEGG MEDI...CUS Database Description General information of database Database name KEGG MEDICUS...ug design Organism Taxonomy Name: Human Taxonomy ID: 9606 Database description KEGG MEDICUS is an integrated...ge inserts) of all marketed drugs in Japan and the USA are integrated with the KEGG DRUG and KEGG DISEASE databases in KEGG MEDI

  5. A review on quantum search algorithms

    Science.gov (United States)

    Giri, Pulak Ranjan; Korepin, Vladimir E.

    2017-12-01

    The use of superposition of states in quantum computation, known as quantum parallelism, has significant advantage in terms of speed over the classical computation. It is evident from the early invented quantum algorithms such as Deutsch's algorithm, Deutsch-Jozsa algorithm and its variation as Bernstein-Vazirani algorithm, Simon algorithm, Shor's algorithms, etc. Quantum parallelism also significantly speeds up the database search algorithm, which is important in computer science because it comes as a subroutine in many important algorithms. Quantum database search of Grover achieves the task of finding the target element in an unsorted database in a time quadratically faster than the classical computer. We review Grover's quantum search algorithms for a singe and multiple target elements in a database. The partial search algorithm of Grover and Radhakrishnan and its optimization by Korepin called GRK algorithm are also discussed.

  6. License - RGP gmap | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...nged without notice. About This Database Database Description Download License Update History of This Database Site Policy | Contact Us License - RGP gmap | LSDB Archive ...

  7. Download - Plabrain DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data List Contact us Plabrain...s Database Database Description Download License Update History of This Database Site Policy | Contact Us Download - Plabrain DB | LSDB Archive ...

  8. License - fRNAdb | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...be changed without notice. About This Database Database Description Download License Update History of This Database Site Policy | Contact Us License - fRNAdb | LSDB Archive ...

  9. License - AT Atlas | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ... might be changed without notice. About This Database Database Description Download License Update History of This Database Site Policy | Contact Us License - AT Atlas | LSDB Archive ...

  10. License - TP Atlas | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ... might be changed without notice. About This Database Database Description Download License Update History of This Database Site Policy | Contact Us License - TP Atlas | LSDB Archive ...

  11. Analysis of lomustine drug content in FDA-approved and compounded lomustine capsules.

    Science.gov (United States)

    KuKanich, Butch; Warner, Matt; Hahn, Kevin

    2017-02-01

    OBJECTIVE To determine the lomustine content (potency) in compounded and FDA-approved lomustine capsules. DESIGN Evaluation study. SAMPLE 2 formulations of lomustine capsules (low dose [7 to 11 mg] and high dose [40 to 48 mg]; 5 capsules/dose/source) from 3 compounders and from 1 manufacturer of FDA-approved capsules. PROCEDURES Lomustine content was measured by use of a validated high-pressure liquid chromatography method. An a priori acceptable range of 90% to 110% of the stated lomustine content was selected on the basis of US Pharmacopeia guidelines. RESULTS The measured amount of lomustine in all compounded capsules was less than the stated content (range, 59% to 95%) and was frequently outside the acceptable range (failure rate, 2/5 to 5/5). Coefficients of variation for lomustine content ranged from 4.1% to 16.7% for compounded low-dose capsules and from 1.1% to 10.8% for compounded high-dose capsules. The measured amount of lomustine in all FDA-approved capsules was slightly above the stated content (range, 104% to 110%) and consistently within the acceptable range. Coefficients of variation for lomustine content were 0.5% for low-dose and 2.3% for high-dose FDA-approved capsules. CONCLUSIONS AND CLINICAL RELEVANCE Compounded lomustine frequently did not contain the stated content of active drug and had a wider range of lomustine content variability than did the FDA-approved product. The sample size was small, and larger studies are needed to confirm these findings; however, we recommend that compounded veterinary formulations of lomustine not be used when appropriate doses can be achieved with FDA-approved capsules or combinations of FDA-approved capsules.

  12. Advancing Product Quality: a Summary of the Inaugural FDA/PQRI Conference.

    Science.gov (United States)

    Yu, Lawrence X; Baker, Jeffrey; Berlam, Susan C; Boam, Ashley; Brandreth, E J; Buhse, Lucinda; Cosgrove, Thomas; Doleski, David; Ensor, Lynne; Famulare, Joseph; Ganapathy, Mohan; Grampp, Gustavo; Hussong, David; Iser, Robert; Johnston, Gordon; Kesisoglou, Filippos; Khan, Mansoor; Kozlowski, Steven; Lacana, Emanuela; Lee, Sau L; Miller, Stephen; Miksinski, Sarah Pope; Moore, Christine M V; Mullin, Theresa; Raju, G K; Raw, Andre; Rosencrance, Susan; Rosolowsky, Mark; Stinavage, Paul; Thomas, Hayden; Wesdyk, Russell; Windisch, Joerg; Vaithiyalingam, Sivakumar

    2015-07-01

    On September 16 and 17, 2014, the Food and Drug Administration (FDA) and Product Quality Research Institute (PQRI) inaugurated their Conference on Evolving Product Quality. The Conference is conceived as an annual forum in which scientists from regulatory agencies, industry, and academia may exchange viewpoints and work together to advance pharmaceutical quality. This Conference Summary Report highlights key topics of this conference, including (1) risk-based approaches to pharmaceutical development, manufacturing, regulatory assessment, and post-approval changes; (2) FDA-proposed quality metrics for products, facilities, and quality management systems; (3) performance-based quality assessment and clinically relevant specifications; (4) recent developments and implementation of continuous manufacturing processes, question-based review, and European Medicines Agency (EMA)-FDA pilot for Quality-by-Design (QbD) applications; and (5) breakthrough therapies, biosimilars, and international harmonization, focusing on ICH M7 and Q3D guidelines. The second FDA/PQRI conference on advancing product quality is planned for October 5-7, 2015.

  13. Evaluation of Federated Searching Options for the School Library

    Science.gov (United States)

    Abercrombie, Sarah E.

    2008-01-01

    Three hosted federated search tools, Follett One Search, Gale PowerSearch Plus, and WebFeat Express, were configured and implemented in a school library. Databases from five vendors and the OPAC were systematically searched. Federated search results were compared with each other and to the results of the same searches in the database's native…

  14. FDA-approved small-molecule kinase inhibitors

    DEFF Research Database (Denmark)

    Wu, Peng; Nielsen, Thomas E.; Clausen, Mads Hartvig

    2015-01-01

    Kinases have emerged as one of the most intensivelypursued targets in current pharmacological research,especially for cancer, due to their critical roles in cellularsignaling. To date, the US FDA has approved 28 smallmoleculekinase inhibitors, half of which were approvedin the past 3 years. While...

  15. Download - SAHG | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...Database Description Download License Update History of This Database Site Policy | Contact Us Download - SAHG | LSDB Archive ...

  16. Download - Metabolonote | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ... Database Description Download License Update History of This Database Site Policy | Contact Us Download - Metabolonote | LSDB Archive ...

  17. Reference - PLACE | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...ailable. Data file File name: place_reference.zip File URL: ftp://ftp.biosciencedbc.jp/archive/place/LATEST/...ber About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Reference - PLACE | LSDB Archive ...

  18. Multilingual access to full text databases

    International Nuclear Information System (INIS)

    Fluhr, C.; Radwan, K.

    1990-05-01

    Many full text databases are available in only one language, or more, they may contain documents in different languages. Even if the user is able to understand the language of the documents in the database, it could be easier for him to express his need in his own language. For the case of databases containing documents in different languages, it is more simple to formulate the query in one language only and to retrieve documents in different languages. This paper present the developments and the first experiments of multilingual search, applied to french-english pair, for text data in nuclear field, based on the system SPIRIT. After reminding the general problems of full text databases search by queries formulated in natural language, we present the methods used to reformulate the queries and show how they can be expanded for multilingual search. The first results on data in nuclear field are presented (AFCEN norms and INIS abstracts). 4 refs

  19. Could FDA approval of pre-exposure prophylaxis make a difference? A qualitative study of PrEP acceptability and FDA perceptions among men who have sex with men.

    Science.gov (United States)

    Underhill, Kristen; Morrow, Kathleen M; Operario, Don; Mayer, Kenneth H

    2014-02-01

    The FDA has approved tenofovir-emtricitabine for use as HIV pre-exposure prophylaxis, but it is unknown how approval may affect PrEP acceptability among US men who have sex with men. We conducted 8 focus groups among 38 Rhode Island MSM, including 3 groups among 16 male sex workers and 5 groups among 22 men in the general MSM community. Participants reported wide-ranging beliefs regarding consequences and meanings of FDA approval. Some participants would not use PrEP without approval, while others perceived approval as irrelevant or less significant than other sources of information. Our results suggest that FDA approval sends a signal that directly shapes PrEP acceptability among some MSM, while indirect influences of approval may affect uptake by others. Efforts to educate MSM about PrEP can increase acceptability by incorporating information about FDA approval, and outreach strategies should consider how this information may factor into personal decisions about PrEP use.

  20. License - GRIPDB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...e Database Description Download License Update History of This Database Site Policy | Contact Us License - GRIPDB | LSDB Archive ...

  1. License - GETDB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...se Database Description Download License Update History of This Database Site Policy | Contact Us License - GETDB | LSDB Archive ...

  2. Ocean Drilling Program: Janus Web Database

    Science.gov (United States)

    JANUS Database Send questions/comments about the online database Request data not available online Janus database Search the ODP/TAMU web site ODP's main web site Janus Data Model Data Migration Overview in Janus Data Types and Examples Leg 199, sunrise. Janus Web Database ODP and IODP data are stored in

  3. Literature database aid

    International Nuclear Information System (INIS)

    Wanderer, J.A.

    1991-01-01

    The booklet is to help with the acquisition of original literature either after a conventional literature search or in particular after a database search. It bridges the gap between abbreviated (short) and original (long) titel. This, together with information on the holdings of technical/scientific libraries, facilitates document delivery. 1500 short titles are listed alphabetically. (orig.) [de

  4. Inspection Database

    Data.gov (United States)

    U.S. Department of Health & Human Services — FDA is disclosing the final inspection classification for inspections related to currently marketed FDA-regulated products. The disclosure of this information is not...

  5. Preference vs. Authority: A Comparison of Student Searching in a Subject-Specific Indexing and Abstracting Database and a Customized Discovery Layer

    Science.gov (United States)

    Dahlen, Sarah P. C.; Hanson, Kathlene

    2017-01-01

    Discovery layers provide a simplified interface for searching library resources. Libraries with limited finances make decisions about retaining indexing and abstracting databases when similar information is available in discovery layers. These decisions should be informed by student success at finding quality information as well as satisfaction…

  6. License - FANTOM5 | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data List Contact us FANTOM....0 International . If you use data from this database, please be sure attribute this database as follows: FANTOM...se Database Description Download License Update History of This Database Site Policy | Contact Us License - FANTOM5 | LSDB Archive ...

  7. Optimization of partial search

    International Nuclear Information System (INIS)

    Korepin, Vladimir E

    2005-01-01

    A quantum Grover search algorithm can find a target item in a database faster than any classical algorithm. One can trade accuracy for speed and find a part of the database (a block) containing the target item even faster; this is partial search. A partial search algorithm was recently suggested by Grover and Radhakrishnan. Here we optimize it. Efficiency of the search algorithm is measured by the number of queries to the oracle. The author suggests a new version of the Grover-Radhakrishnan algorithm which uses a minimal number of such queries. The algorithm can run on the same hardware that is used for the usual Grover algorithm. (letter to the editor)

  8. Exon - ASTRA | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...ontents Exons in variants Data file File name: astra_exon.zip File URL: ftp://ftp.biosciencedbc.jp/archive/a... About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Exon - ASTRA | LSDB Archive ...

  9. Scopus database: a review.

    Science.gov (United States)

    Burnham, Judy F

    2006-03-08

    The Scopus database provides access to STM journal articles and the references included in those articles, allowing the searcher to search both forward and backward in time. The database can be used for collection development as well as for research. This review provides information on the key points of the database and compares it to Web of Science. Neither database is inclusive, but complements each other. If a library can only afford one, choice must be based in institutional needs.

  10. Evaluating eating behavior treatments by FDA standards

    Directory of Open Access Journals (Sweden)

    A. Janet eTomiyama

    2014-01-01

    Full Text Available Behavioral treatments for obesity are not evaluated by the same criteria as pharmaceutical drugs, even though treatments such as low-calorie dieting are widely prescribed, require the patients’ time and investment, and may have risks. The Food and Drug Administration (FDA has a procedure for evaluating drugs, in which drugmakers must answer the following questions: (1 Is the treatment safe? (2 How dangerous is the condition the intervention is treating? (3 Is the treatment effective? (4 Is the treatment safe and effective for large numbers of people? We argue that using this framework to evaluate behavioral interventions could help identify unanswered research questions on their efficacy and effectiveness, and we use the example of low-calorie dieting to illustrate how FDA criteria might be applied in the context of behavioral medicine.

  11. Using the TIGR gene index databases for biological discovery.

    Science.gov (United States)

    Lee, Yuandan; Quackenbush, John

    2003-11-01

    The TIGR Gene Index web pages provide access to analyses of ESTs and gene sequences for nearly 60 species, as well as a number of resources derived from these. Each species-specific database is presented using a common format with a homepage. A variety of methods exist that allow users to search each species-specific database. Methods implemented currently include nucleotide or protein sequence queries using WU-BLAST, text-based searches using various sequence identifiers, searches by gene, tissue and library name, and searches using functional classes through Gene Ontology assignments. This protocol provides guidance for using the Gene Index Databases to extract information.

  12. Astronomical databases of Nikolaev Observatory

    Science.gov (United States)

    Protsyuk, Y.; Mazhaev, A.

    2008-07-01

    Several astronomical databases were created at Nikolaev Observatory during the last years. The databases are built by using MySQL search engine and PHP scripts. They are available on NAO web-site http://www.mao.nikolaev.ua.

  13. 78 FR 58545 - Global Unique Device Identification Database; Draft Guidance for Industry; Availability

    Science.gov (United States)

    2013-09-24

    ... manufacturer) will interface with the GUDID, as well as information on the database elements that must be... information in the proposed rule are subject to review by the Office of Management and Budget (OMB) under the... DEPARTMENT OF HEALTH AND HUMAN SERVICES Food and Drug Administration [Docket No. FDA-2013-D-0636...

  14. Access to Investigational Drugs: FDA Expanded Access Programs or "Right-to-Try" Legislation?

    Science.gov (United States)

    Holbein, M E Blair; Berglund, Jelena P; Weatherwax, Kevin; Gerber, David E; Adamo, Joan E

    2015-10-01

    The Food and Drug Administration Expanded Access (EA) program and "Right-to-Try" legislation aim to provide seriously ill patients who have no other comparable treatment options to gain access to investigational drugs and biological agents. Physicians and institutions need to understand these programs to respond to questions and requests for access. FDA EA programs and state and federal legislative efforts to provide investigational products to patients by circumventing FDA regulations were summarized and compared. The FDA EA program includes Single Patient-Investigational New Drug (SP-IND), Emergency SP-IND, Intermediate Sized Population IND, and Treatment IND. Approval rates for all categories exceed 99%. Approval requires FDA and Institutional Review Board (IRB) approval, and cooperation of the pharmaceutical partner is essential. "Right-to-Try" legislation bypasses some of these steps, but provides no regulatory or safety oversight. The FDA EA program is a reasonable option for patients for whom all other therapeutic interventions have failed. The SP-IND not only provides patient access to new drugs, but also maintains a balance between immediacy and necessary patient protection. Rather than circumventing existing FDA regulations through proposed legislation, it seems more judicious to provide the knowledge and means to meet the EA requirements. © 2015 Wiley Periodicals, Inc.

  15. Effective Image Database Search via Dimensionality Reduction

    DEFF Research Database (Denmark)

    Dahl, Anders Bjorholm; Aanæs, Henrik

    2008-01-01

    Image search using the bag-of-words image representation is investigated further in this paper. This approach has shown promising results for large scale image collections making it relevant for Internet applications. The steps involved in the bag-of-words approach are feature extraction, vocabul......Image search using the bag-of-words image representation is investigated further in this paper. This approach has shown promising results for large scale image collections making it relevant for Internet applications. The steps involved in the bag-of-words approach are feature extraction......, vocabulary building, and searching with a query image. It is important to keep the computational cost low through all steps. In this paper we focus on the efficiency of the technique. To do that we substantially reduce the dimensionality of the features by the use of PCA and addition of color. Building...... of the visual vocabulary is typically done using k-means. We investigate a clustering algorithm based on the leader follower principle (LF-clustering), in which the number of clusters is not fixed. The adaptive nature of LF-clustering is shown to improve the quality of the visual vocabulary using this...

  16. International patent applications for non-injectable naloxone for opioid overdose reversal: Exploratory search and retrieve analysis of the PatentScope database.

    Science.gov (United States)

    McDonald, Rebecca; Danielsson Glende, Øyvind; Dale, Ola; Strang, John

    2018-02-01

    Non-injectable naloxone formulations are being developed for opioid overdose reversal, but only limited data have been published in the peer-reviewed domain. Through examination of a hitherto-unsearched database, we expand public knowledge of non-injectable formulations, tracing their development and novelty, with the aim to describe and compare their pharmacokinetic properties. (i) The PatentScope database of the World Intellectual Property Organization was searched for relevant English-language patent applications; (ii) Pharmacokinetic data were extracted, collated and analysed; (iii) PubMed was searched using Boolean search query '(nasal OR intranasal OR nose OR buccal OR sublingual) AND naloxone AND pharmacokinetics'. Five hundred and twenty-two PatentScope and 56 PubMed records were identified: three published international patent applications and five peer-reviewed papers were eligible. Pharmacokinetic data were available for intranasal, sublingual, and reference routes. Highly concentrated formulations (10-40 mg mL -1 ) had been developed and tested. Sublingual bioavailability was very low (1%; relative to intravenous). Non-concentrated intranasal spray (1 mg mL -1 ; 1 mL per nostril) had low bioavailability (11%). Concentrated intranasal formulations (≥10 mg mL -1 ) had bioavailability of 21-42% (relative to intravenous) and 26-57% (relative to intramuscular), with peak concentrations (dose-adjusted C max  = 0.8-1.7 ng mL -1 ) reached in 19-30 min (t max ). Exploratory analysis identified intranasal bioavailability as associated positively with dose and negatively with volume. We find consistent direction of development of intranasal sprays to high-concentration, low-volume formulations with bioavailability in the 20-60% range. These have potential to deliver a therapeutic dose in 0.1 mL volume. [McDonald R, Danielsson Glende Ø, Dale O, Strang J. International patent applications for non-injectable naloxone for opioid overdose reversal

  17. Database in Artificial Intelligence.

    Science.gov (United States)

    Wilkinson, Julia

    1986-01-01

    Describes a specialist bibliographic database of literature in the field of artificial intelligence created by the Turing Institute (Glasgow, Scotland) using the BRS/Search information retrieval software. The subscription method for end-users--i.e., annual fee entitles user to unlimited access to database, document provision, and printed awareness…

  18. An effective suggestion method for keyword search of databases

    KAUST Repository

    Huang, Hai; Chen, Zonghai; Liu, Chengfei; Huang, He; Zhang, Xiangliang

    2016-01-01

    This paper solves the problem of providing high-quality suggestions for user keyword queries over databases. With the assumption that the returned suggestions are independent, existing query suggestion methods over databases score candidate

  19. 76 FR 30175 - Draft Guidance for Clinical Investigators, Industry, and FDA Staff: Financial Disclosure by...

    Science.gov (United States)

    2011-05-24

    ... consider public release of financial disclosure information related to an approved marketing application...] (Formerly FDA-1999-D-0792) Draft Guidance for Clinical Investigators, Industry, and FDA Staff: Financial... entitled ``Guidance for Clinical Investigators, Industry, and FDA Staff: Financial Disclosure by Clinical...

  20. Undergraduates Prefer Federated Searching to Searching Databases Individually. A Review of: Belliston, C. Jeffrey, Jared L. Howland, & Brian C. Roberts. “Undergraduate Use of Federated Searching: A Survey of Preferences and Perceptions of Value-Added Functionality.” College & Research Libraries 68.6 (Nov. 2007: 472-86.

    Directory of Open Access Journals (Sweden)

    Genevieve Gore

    2008-09-01

    Full Text Available Objective – To determine whether use offederated searching by undergraduates saves time, meets their information needs, is preferred over searching databases individually, and provides results of higher quality. Design – Crossover study.Setting – Three American universities, all members of the Consortium of Church Libraries & Archives (CCLA: BYU (Brigham Young University, a large research university; BYUH (Brigham Young University – Hawaii, a small baccalaureate college; and BYUI (Brigham Young University – Idaho, a large baccalaureate collegeSubjects – Ninety-five participants recruited via e-mail invitations sent to a random sample of currently enrolled undergraduates at BYU, BYUH, and BYUI.Methods – Participants were given written directions to complete a literature search for journal articles on two biology-related topics using two search methods: 1. federated searching with WebFeat® (implemented in the same way for this study at the three universities and 2. a hyperlinked list of databases to search individually. Both methods used the same set of seven databases. Each topic was assigned in random order to one of the two search methods, also assigned in random order, for a total of two searches per participant. The time to complete the searches was recorded. Students compiled their list of citations, which were later normalized and graded. To analyze the quality of the citations, one quantitative rubric was created by librarians and one qualitative rubric was approved by a faculty member at BYU. The librarian-created rubric included the journal impact factor (from ISI’s Journal Citation Reports®, the proportion of citations from peer-reviewed journals (determined from Ulrichsweb.com™ to total citations, and the timeliness of the articles. The faculty-approved rubric included three criteria: relevance to the topic, quality of the individual citations (good quality: primary research results, peer-reviewed sources, and

  1. Flat Files - JSNP | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ... Data file File name: jsnp_flat_files File URL: ftp://ftp.biosciencedbc.jp/archiv...his Database Database Description Download License Update History of This Database Site Policy | Contact Us Flat Files - JSNP | LSDB Archive ...

  2. Ariadne: a database search engine for identification and chemical analysis of RNA using tandem mass spectrometry data.

    Science.gov (United States)

    Nakayama, Hiroshi; Akiyama, Misaki; Taoka, Masato; Yamauchi, Yoshio; Nobe, Yuko; Ishikawa, Hideaki; Takahashi, Nobuhiro; Isobe, Toshiaki

    2009-04-01

    We present here a method to correlate tandem mass spectra of sample RNA nucleolytic fragments with an RNA nucleotide sequence in a DNA/RNA sequence database, thereby allowing tandem mass spectrometry (MS/MS)-based identification of RNA in biological samples. Ariadne, a unique web-based database search engine, identifies RNA by two probability-based evaluation steps of MS/MS data. In the first step, the software evaluates the matches between the masses of product ions generated by MS/MS of an RNase digest of sample RNA and those calculated from a candidate nucleotide sequence in a DNA/RNA sequence database, which then predicts the nucleotide sequences of these RNase fragments. In the second step, the candidate sequences are mapped for all RNA entries in the database, and each entry is scored for a function of occurrences of the candidate sequences to identify a particular RNA. Ariadne can also predict post-transcriptional modifications of RNA, such as methylation of nucleotide bases and/or ribose, by estimating mass shifts from the theoretical mass values. The method was validated with MS/MS data of RNase T1 digests of in vitro transcripts. It was applied successfully to identify an unknown RNA component in a tRNA mixture and to analyze post-transcriptional modification in yeast tRNA(Phe-1).

  3. Personalized Search

    CERN Document Server

    AUTHOR|(SzGeCERN)749939

    2015-01-01

    As the volume of electronically available information grows, relevant items become harder to find. This work presents an approach to personalizing search results in scientific publication databases. This work focuses on re-ranking search results from existing search engines like Solr or ElasticSearch. This work also includes the development of Obelix, a new recommendation system used to re-rank search results. The project was proposed and performed at CERN, using the scientific publications available on the CERN Document Server (CDS). This work experiments with re-ranking using offline and online evaluation of users and documents in CDS. The experiments conclude that the personalized search result outperform both latest first and word similarity in terms of click position in the search result for global search in CDS.

  4. Atomic Spectra Database (ASD)

    Science.gov (United States)

    SRD 78 NIST Atomic Spectra Database (ASD) (Web, free access)   This database provides access and search capability for NIST critically evaluated data on atomic energy levels, wavelengths, and transition probabilities that are reasonably up-to-date. The NIST Atomic Spectroscopy Data Center has carried out these critical compilations.

  5. Uploading, Searching and Visualizing of Paleomagnetic and Rock Magnetic Data in the Online MagIC Database

    Science.gov (United States)

    Minnett, R.; Koppers, A.; Tauxe, L.; Constable, C.; Donadini, F.

    2007-12-01

    The Magnetics Information Consortium (MagIC) is commissioned to implement and maintain an online portal to a relational database populated by both rock and paleomagnetic data. The goal of MagIC is to archive all available measurements and derived properties from paleomagnetic studies of directions and intensities, and for rock magnetic experiments (hysteresis, remanence, susceptibility, anisotropy). MagIC is hosted under EarthRef.org at http://earthref.org/MAGIC/ and will soon implement two search nodes, one for paleomagnetism and one for rock magnetism. Currently the PMAG node is operational. Both nodes provide query building based on location, reference, methods applied, material type and geological age, as well as a visual map interface to browse and select locations. Users can also browse the database by data type or by data compilation to view all contributions associated with well known earlier collections like PINT, GMPDB or PSVRL. The query result set is displayed in a digestible tabular format allowing the user to descend from locations to sites, samples, specimens and measurements. At each stage, the result set can be saved and, where appropriate, can be visualized by plotting global location maps, equal area, XY, age, and depth plots, or typical Zijderveld, hysteresis, magnetization and remanence diagrams. User contributions to the MagIC database are critical to achieving a useful research tool. We have developed a standard data and metadata template (version 2.3) that can be used to format and upload all data at the time of publication in Earth Science journals. Software tools are provided to facilitate population of these templates within Microsoft Excel. These tools allow for the import/export of text files and provide advanced functionality to manage and edit the data, and to perform various internal checks to maintain data integrity and prepare for uploading. The MagIC Contribution Wizard at http://earthref.org/MAGIC/upload.htm executes the upload

  6. FDA actions against health economic promotions, 2002-2011.

    Science.gov (United States)

    Neumann, Peter J; Bliss, Sarah K

    2012-01-01

    To investigate Food and Drug Administration (FDA) regulatory actions against drug companies' health economic promotions from 2002 through 2011 to understand how frequently and in what circumstances the agency has considered such promotions false or misleading. We reviewed all warning letters and notices of violation ("untitled letters") issued by the FDA's Division of Drug Marketing, Advertising and Communications (DDMAC) to pharmaceutical companies from January 2002 through December 2011. We analyzed letters containing a violation related to "health economic promotion," defined according to one of several categories (e.g., implied claims of cost savings due to work productivity or economic claims containing unsupported statements about effectiveness or safety). We also collected information on factors such as the indication and type of media involved and whether the letter referenced Section 114 of the Food and Drug Administration Modernization Act. Of 291 DDMAC letters sent to pharmaceutical companies during the study period, 35 (12%) cited a health economic violation. The most common type of violation cited was an implied claim of cost savings due to work productivity or functioning (found in 20 letters) and economic claims containing unsubstantiated comparative claims of effectiveness, safety, or interchangeability (7 letters). The violations covered various indications, mostly commonly psychiatric disorders (6 letters) and pain (6 letters). No DDMAC letter pertained to Food and Drug Administration Modernization Act Section 114. The FDA has cited inappropriate health economic promotions in roughly 12% of the letters issued by the DDMAC. The letters highlight drug companies' interest in promoting the value of their products and the FDA's concerns in certain cases about the lack of supporting evidence. Copyright © 2012 International Society for Pharmacoeconomics and Outcomes Research (ISPOR). Published by Elsevier Inc. All rights reserved.

  7. Protein - AT Atlas | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ..._protein.zip File URL: ftp://ftp.biosciencedbc.jp/archive/at_atlas/LATEST/at_atla...About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Protein - AT Atlas | LSDB Archive ...

  8. Download - FANTOM5 | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data List Contact us FANTOM... and CAGE TSS aggregation fantom5_new_experimental_details.zip (273 KB) basic (1.3 TB) Simple search and dow...nload 3 (reprocessed)HeliscopeCAGE sequencing, Delve mapping and CAGE TSS aggregation fantom5_rp_exp_details...access [here]. About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Download - FANTOM5 | LSDB Archive ...

  9. License - tRNADB-CE | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data List Contact us tRNAD...-Share Alike 2.1 Japan. If you use data from this database, please be sure attribute this database as follows: tRNAD...: About This Database Database Description Download License Update History of This Database Site Policy | Contact Us License - tRNADB-CE | LSDB Archive ...

  10. Home | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available ple Search Original Site Database Center for Life Science Kousaku Okubo organ human The dictionary-type data...-SA Detail Taxonomy Icon Taxonomy Icon Download | Simple Search Original Site National Bioscience Database Center Kousaku Okubo...enter for Life Science Kousaku Okubo Dictionary 9 species (human, mouse, rat, zeb

  11. Searching the protein structure database for ligand-binding site similarities using CPASS v.2

    Directory of Open Access Journals (Sweden)

    Caprez Adam

    2011-01-01

    Full Text Available Abstract Background A recent analysis of protein sequences deposited in the NCBI RefSeq database indicates that ~8.5 million protein sequences are encoded in prokaryotic and eukaryotic genomes, where ~30% are explicitly annotated as "hypothetical" or "uncharacterized" protein. Our Comparison of Protein Active-Site Structures (CPASS v.2 database and software compares the sequence and structural characteristics of experimentally determined ligand binding sites to infer a functional relationship in the absence of global sequence or structure similarity. CPASS is an important component of our Functional Annotation Screening Technology by NMR (FAST-NMR protocol and has been successfully applied to aid the annotation of a number of proteins of unknown function. Findings We report a major upgrade to our CPASS software and database that significantly improves its broad utility. CPASS v.2 is designed with a layered architecture to increase flexibility and portability that also enables job distribution over the Open Science Grid (OSG to increase speed. Similarly, the CPASS interface was enhanced to provide more user flexibility in submitting a CPASS query. CPASS v.2 now allows for both automatic and manual definition of ligand-binding sites and permits pair-wise, one versus all, one versus list, or list versus list comparisons. Solvent accessible surface area, ligand root-mean square difference, and Cβ distances have been incorporated into the CPASS similarity function to improve the quality of the results. The CPASS database has also been updated. Conclusions CPASS v.2 is more than an order of magnitude faster than the original implementation, and allows for multiple simultaneous job submissions. Similarly, the CPASS database of ligand-defined binding sites has increased in size by ~ 38%, dramatically increasing the likelihood of a positive search result. The modification to the CPASS similarity function is effective in reducing CPASS similarity scores

  12. Download - eSOL | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...Database Description Download License Update History of This Database Site Policy | Contact Us Download - eSOL | LSDB Archive ...

  13. Online Petroleum Industry Bibliographic Databases: A Review.

    Science.gov (United States)

    Anderson, Margaret B.

    This paper discusses the present status of the bibliographic database industry, reviews the development of online databases of interest to the petroleum industry, and considers future developments in online searching and their effect on libraries and information centers. Three groups of databases are described: (1) databases developed by the…

  14. License - KEGG MEDICUS | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] English ]; } else if ( url.search(//en//) != -1 ) { url = url.replace(/...switchLanguage; BLAST Search Image Search Home About Archive Update History Data List Contact us KEGG MEDI...ion-NonCommercial-NoDerivs 2.1 Japan. If you use data from this database, please be sure attribute this data...whole of this database, and acquire data; and freely redistribute part or whole of the data from this databa...This Database Site Policy | Contact Us License - KEGG MEDICUS | LSDB Archive ...

  15. Status report on nuclear power - information from STN databases

    International Nuclear Information System (INIS)

    Prinz, H.

    1995-01-01

    The worldwide future of nuclear power as seen about 25 years ago is presented based on a literature search in the INIS database. The role of nuclear power today, after TMI and Chernobyl, in energy supplies and in combating the greehouse effect is evaluated by literature searches in STN databases (e.g. INIS, ETDE, COMPENDEX, CA, ULIDAT, INSPEC). An evaluation is given of the different information contents of bibliographic databases such as INIS and pure information databases such as NLDB. (orig./HP)

  16. ORF information - KOME | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ... File URL: ftp://ftp.biosciencedbc.jp/archive/kome/LATEST/kome_orf_infomation.zip File size: 526 KB Simple s...ut This Database Database Description Download License Update History of This Database Site Policy | Contact Us ORF information - KOME | LSDB Archive ...

  17. EST data - RED | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...st.zip File URL: ftp://ftp.biosciencedbc.jp/archive/red/LATEST/red_est.zip File size: 629 KB Simple search U...ase Database Description Download License Update History of This Database Site Policy | Contact Us EST data - RED | LSDB Archive ...

  18. Accelerating Information Retrieval from Profile Hidden Markov Model Databases.

    Science.gov (United States)

    Tamimi, Ahmad; Ashhab, Yaqoub; Tamimi, Hashem

    2016-01-01

    Profile Hidden Markov Model (Profile-HMM) is an efficient statistical approach to represent protein families. Currently, several databases maintain valuable protein sequence information as profile-HMMs. There is an increasing interest to improve the efficiency of searching Profile-HMM databases to detect sequence-profile or profile-profile homology. However, most efforts to enhance searching efficiency have been focusing on improving the alignment algorithms. Although the performance of these algorithms is fairly acceptable, the growing size of these databases, as well as the increasing demand for using batch query searching approach, are strong motivations that call for further enhancement of information retrieval from profile-HMM databases. This work presents a heuristic method to accelerate the current profile-HMM homology searching approaches. The method works by cluster-based remodeling of the database to reduce the search space, rather than focusing on the alignment algorithms. Using different clustering techniques, 4284 TIGRFAMs profiles were clustered based on their similarities. A representative for each cluster was assigned. To enhance sensitivity, we proposed an extended step that allows overlapping among clusters. A validation benchmark of 6000 randomly selected protein sequences was used to query the clustered profiles. To evaluate the efficiency of our approach, speed and recall values were measured and compared with the sequential search approach. Using hierarchical, k-means, and connected component clustering techniques followed by the extended overlapping step, we obtained an average reduction in time of 41%, and an average recall of 96%. Our results demonstrate that representation of profile-HMMs using a clustering-based approach can significantly accelerate data retrieval from profile-HMM databases.

  19. Examples how to use atomic and molecular databases

    International Nuclear Information System (INIS)

    Murakami, Izumi

    2012-01-01

    As examples how to use atomic and molecular databases, atomic spectra database (ASD) and molecular chemical kinetics database of National Institute of Standards and Technology (NIST), collision cross sections of National Institute of Fusion Science (NIFS), Open-Atomic Data and Analysis Structure (ADAS) and chemical reaction rate coefficients of GRI-Mech were presented. Sorting method differed in each database and several options were prepared. Atomic wavelengths/transition probabilities and electron collision ionization, excitation and recombination cross sections/rate coefficients were simply searched with just specifying atom or ion using a general internet search engine (GENIE) of IAEA. (T. Tanaka)

  20. Adherence of pharmaceutical advertisements in medical journals to FDA guidelines and content for safe prescribing.

    Science.gov (United States)

    Korenstein, Deborah; Keyhani, Salomeh; Mendelson, Ali; Ross, Joseph S

    2011-01-01

    Physician-directed pharmaceutical advertising is regulated in the United States by the Food and Drug Administration (FDA); adherence to current FDA guidelines is unknown. Our objective was to determine adherence rates of physician-directed print advertisements in biomedical journals to FDA guidelines and describe content important for safe prescribing. Cross-sectional analysis of November 2008 pharmaceutical advertisements within top U.S.-based biomedical journals publishing original research. We excluded advertisements for devices, over the counter medications, and disease awareness. We utilized FDA guideline items identifying unique forms of advertisement bias to categorize advertisements as adherent to FDA guidelines, possibly non-adherent to at least 1 item, or non-adherent to at least 1 item. We also evaluated advertisement content important for safe prescribing, including benefit quantification, risk information and verifiable references. All advertisements were evaluated by 2 or more investigators, with differences resolved by discussion. Twelve journals met inclusion criteria. Nine contained pharmaceutical advertisements, including 192 advertisements for 82 unique products; median 2 per product (range 1-14). Six "teaser" advertisements presented only drug names, leaving 83 full unique advertisements. Fifteen advertisements (18.1%) adhered to all FDA guidelines, 41 (49.4%) were non-adherent with at least one form of FDA-described bias, and 27 (32.5%) were possibly non-adherent due to incomplete information. Content important for safe prescribing was often incomplete; 57.8% of advertisements did not quantify serious risks, 48.2% lacked verifiable references and 28.9% failed to present adequate efficacy quantification. Study limitations included its focus on advertisements from a single month, the subjectivity of FDA guidelines themselves, and the necessary subjectivity of determinations of adherence. Few physician-directed print pharmaceutical advertisements

  1. Adherence of pharmaceutical advertisements in medical journals to FDA guidelines and content for safe prescribing.

    Directory of Open Access Journals (Sweden)

    Deborah Korenstein

    Full Text Available Physician-directed pharmaceutical advertising is regulated in the United States by the Food and Drug Administration (FDA; adherence to current FDA guidelines is unknown. Our objective was to determine adherence rates of physician-directed print advertisements in biomedical journals to FDA guidelines and describe content important for safe prescribing.Cross-sectional analysis of November 2008 pharmaceutical advertisements within top U.S.-based biomedical journals publishing original research. We excluded advertisements for devices, over the counter medications, and disease awareness. We utilized FDA guideline items identifying unique forms of advertisement bias to categorize advertisements as adherent to FDA guidelines, possibly non-adherent to at least 1 item, or non-adherent to at least 1 item. We also evaluated advertisement content important for safe prescribing, including benefit quantification, risk information and verifiable references. All advertisements were evaluated by 2 or more investigators, with differences resolved by discussion. Twelve journals met inclusion criteria. Nine contained pharmaceutical advertisements, including 192 advertisements for 82 unique products; median 2 per product (range 1-14. Six "teaser" advertisements presented only drug names, leaving 83 full unique advertisements. Fifteen advertisements (18.1% adhered to all FDA guidelines, 41 (49.4% were non-adherent with at least one form of FDA-described bias, and 27 (32.5% were possibly non-adherent due to incomplete information. Content important for safe prescribing was often incomplete; 57.8% of advertisements did not quantify serious risks, 48.2% lacked verifiable references and 28.9% failed to present adequate efficacy quantification. Study limitations included its focus on advertisements from a single month, the subjectivity of FDA guidelines themselves, and the necessary subjectivity of determinations of adherence.Few physician-directed print pharmaceutical

  2. FDA regulations for commercial food irradiation

    International Nuclear Information System (INIS)

    Takeguchi, C.A.

    1985-01-01

    The Food and Drug Administration published an Advance Notice of Proposed Rulemaking (ANPR) on food irradiation on March 27, 1981 (FDA, 1981). The next step in the rulemaking process is a proposed rule that will deal with low-dose irradiation of certain foods and high-dose irradiation of spices. The status of the proposed regulation is discussed

  3. Mapping data - KOME | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...tional Rice Genome Sequencing Project (IRGSP) Data file File name: kome_mapping_data.zip File URL: ftp://ftp.biosciencedbc.jp/archiv...(Transcriptional Unit) About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Mapping data - KOME | LSDB Archive ...

  4. Spot table - RPD | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...d_spot.zip File URL: ftp://ftp.biosciencedbc.jp/archive/rpd/LATEST/rpd_spot.zip F... cDNA. (multiple entries) About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Spot table - RPD | LSDB Archive ...

  5. About Libraries - AcEST | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...ormat text file. Data file File name: acest_library.zip File URL: ftp://ftp.biosciencedbc.jp/archive/acest/L...ATEST/acest_library.zip File size: 2KB Simple search URL http://togodb.biosciencedbc.jp/togodb/view/archiv...s Database Database Description Download License Update History of This Database Site Policy | Contact Us About Libraries - AcEST | LSDB Archive ...

  6. License - Plabrain DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data List Contact us Plabrain... Alike 2.1 Japan . If you use data from this database, please be sure attribute this database as follows: Plabrain...of this database (http://dbarchive.lifesciencedb.jp/english/en/plabrain-db/desc.html) in the article or pape...se Description Download License Update History of This Database Site Policy | Contact Us License - Plabrain DB | LSDB Archive ...

  7. FDA Regulation of Clinical Applications of CRISPR-CAS Gene-Editing Technology.

    Science.gov (United States)

    Grant, Evita V

    Scientists have repurposed an adaptive immune system of single cell organisms to create a new type of gene-editing tool: CRISPR (clustered regularly interspaced short palindromic repeats)-Cas technology. Scientists in China have reported its use in the genome modification of non-viable human embryos. This has ignited a spirited debate about the moral, ethical, scientific, and social implications of human germline genome engineering. There have also been calls for regulations; however, FDA has yet to formally announce its oversight of clinical applications of CRISPR-Cas systems. This paper reviews FDA regulation of previously controversial biotechnology breakthroughs, recombinant DNA and human cloning. It then shows that FDA is well positioned to regulate CRISPR-Cas clinical applications, due to its legislative mandates, its existing regulatory frameworks for gene therapies and assisted reproductive technologies, and other considerations.

  8. Spatial search by quantum walk

    International Nuclear Information System (INIS)

    Childs, Andrew M.; Goldstone, Jeffrey

    2004-01-01

    Grover's quantum search algorithm provides a way to speed up combinatorial search, but is not directly applicable to searching a physical database. Nevertheless, Aaronson and Ambainis showed that a database of N items laid out in d spatial dimensions can be searched in time of order √(N) for d>2, and in time of order √(N) poly(log N) for d=2. We consider an alternative search algorithm based on a continuous-time quantum walk on a graph. The case of the complete graph gives the continuous-time search algorithm of Farhi and Gutmann, and other previously known results can be used to show that √(N) speedup can also be achieved on the hypercube. We show that full √(N) speedup can be achieved on a d-dimensional periodic lattice for d>4. In d=4, the quantum walk search algorithm takes time of order √(N) poly(log N), and in d<4, the algorithm does not provide substantial speedup

  9. Access to Investigational Drugs: FDA Expanded Access Programs or “Right‐to‐Try” Legislation?

    Science.gov (United States)

    Berglund, Jelena P.; Weatherwax, Kevin; Gerber, David E.; Adamo, Joan E.

    2015-01-01

    Abstract Purpose The Food and Drug Administration Expanded Access (EA) program and “Right‐to‐Try” legislation aim to provide seriously ill patients who have no other comparable treatment options to gain access to investigational drugs and biological agents. Physicians and institutions need to understand these programs to respond to questions and requests for access. Methods FDA EA programs and state and federal legislative efforts to provide investigational products to patients by circumventing FDA regulations were summarized and compared. Results The FDA EA program includes Single Patient‐Investigational New Drug (SP‐IND), Emergency SP‐IND, Intermediate Sized Population IND, and Treatment IND. Approval rates for all categories exceed 99%. Approval requires FDA and Institutional Review Board (IRB) approval, and cooperation of the pharmaceutical partner is essential. “Right‐to‐Try” legislation bypasses some of these steps, but provides no regulatory or safety oversight. Conclusion The FDA EA program is a reasonable option for patients for whom all other therapeutic interventions have failed. The SP‐IND not only provides patient access to new drugs, but also maintains a balance between immediacy and necessary patient protection. Rather than circumventing existing FDA regulations through proposed legislation, it seems more judicious to provide the knowledge and means to meet the EA requirements. PMID:25588691

  10. Integrating Variances into an Analytical Database

    Science.gov (United States)

    Sanchez, Carlos

    2010-01-01

    For this project, I enrolled in numerous SATERN courses that taught the basics of database programming. These include: Basic Access 2007 Forms, Introduction to Database Systems, Overview of Database Design, and others. My main job was to create an analytical database that can handle many stored forms and make it easy to interpret and organize. Additionally, I helped improve an existing database and populate it with information. These databases were designed to be used with data from Safety Variances and DCR forms. The research consisted of analyzing the database and comparing the data to find out which entries were repeated the most. If an entry happened to be repeated several times in the database, that would mean that the rule or requirement targeted by that variance has been bypassed many times already and so the requirement may not really be needed, but rather should be changed to allow the variance's conditions permanently. This project did not only restrict itself to the design and development of the database system, but also worked on exporting the data from the database to a different format (e.g. Excel or Word) so it could be analyzed in a simpler fashion. Thanks to the change in format, the data was organized in a spreadsheet that made it possible to sort the data by categories or types and helped speed up searches. Once my work with the database was done, the records of variances could be arranged so that they were displayed in numerical order, or one could search for a specific document targeted by the variances and restrict the search to only include variances that modified a specific requirement. A great part that contributed to my learning was SATERN, NASA's resource for education. Thanks to the SATERN online courses I took over the summer, I was able to learn many new things about computers and databases and also go more in depth into topics I already knew about.

  11. Standardization of Keyword Search Mode

    Science.gov (United States)

    Su, Di

    2010-01-01

    In spite of its popularity, keyword search mode has not been standardized. Though information professionals are quick to adapt to various presentations of keyword search mode, novice end-users may find keyword search confusing. This article compares keyword search mode in some major reference databases and calls for standardization. (Contains 3…

  12. Custom Search Engines: Tools & Tips

    Science.gov (United States)

    Notess, Greg R.

    2008-01-01

    Few have the resources to build a Google or Yahoo! from scratch. Yet anyone can build a search engine based on a subset of the large search engines' databases. Use Google Custom Search Engine or Yahoo! Search Builder or any of the other similar programs to create a vertical search engine targeting sites of interest to users. The basic steps to…

  13. Small-molecule kinase inhibitors: an analysis of FDA-approved drugs

    DEFF Research Database (Denmark)

    Wu, Peng; Nielsen, Thomas Eiland; Clausen, Mads Hartvig

    2016-01-01

    Small-molecule kinase inhibitors (SMKIs), 28 of which are approved by the US Food and Drug Administration (FDA), have been actively pursued as promising targeted therapeutics. Here, we assess the key structural and physicochemical properties, target selectivity and mechanism of function, and ther......Small-molecule kinase inhibitors (SMKIs), 28 of which are approved by the US Food and Drug Administration (FDA), have been actively pursued as promising targeted therapeutics. Here, we assess the key structural and physicochemical properties, target selectivity and mechanism of function...

  14. PSCID List - PSCDB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...t.zip File URL: ftp://ftp.biosciencedbc.jp/archive/pscdb/LATEST/pscdb_pscid_list.zip File size: 24.4 KB Simp...nd-binding sites About This Database Database Description Download License Update History of This Database Site Policy | Contact Us PSCID List - PSCDB | LSDB Archive ...

  15. Subject Retrieval from Full-Text Databases in the Humanities

    Science.gov (United States)

    East, John W.

    2007-01-01

    This paper examines the problems involved in subject retrieval from full-text databases of secondary materials in the humanities. Ten such databases were studied and their search functionality evaluated, focusing on factors such as Boolean operators, document surrogates, limiting by subject area, proximity operators, phrase searching, wildcards,…

  16. JICST Factual Database(2)

    Science.gov (United States)

    Araki, Keisuke

    The computer programme, which builds atom-bond connection tables from nomenclatures, is developed. Chemical substances with their nomenclature and varieties of trivial names or experimental code numbers are inputted. The chemical structures of the database are stereospecifically stored and are able to be searched and displayed according to stereochemistry. Source data are from laws and regulations of Japan, RTECS of US and so on. The database plays a central role within the integrated fact database service of JICST and makes interrelational retrieval possible.

  17. Accelerating Information Retrieval from Profile Hidden Markov Model Databases.

    Directory of Open Access Journals (Sweden)

    Ahmad Tamimi

    Full Text Available Profile Hidden Markov Model (Profile-HMM is an efficient statistical approach to represent protein families. Currently, several databases maintain valuable protein sequence information as profile-HMMs. There is an increasing interest to improve the efficiency of searching Profile-HMM databases to detect sequence-profile or profile-profile homology. However, most efforts to enhance searching efficiency have been focusing on improving the alignment algorithms. Although the performance of these algorithms is fairly acceptable, the growing size of these databases, as well as the increasing demand for using batch query searching approach, are strong motivations that call for further enhancement of information retrieval from profile-HMM databases. This work presents a heuristic method to accelerate the current profile-HMM homology searching approaches. The method works by cluster-based remodeling of the database to reduce the search space, rather than focusing on the alignment algorithms. Using different clustering techniques, 4284 TIGRFAMs profiles were clustered based on their similarities. A representative for each cluster was assigned. To enhance sensitivity, we proposed an extended step that allows overlapping among clusters. A validation benchmark of 6000 randomly selected protein sequences was used to query the clustered profiles. To evaluate the efficiency of our approach, speed and recall values were measured and compared with the sequential search approach. Using hierarchical, k-means, and connected component clustering techniques followed by the extended overlapping step, we obtained an average reduction in time of 41%, and an average recall of 96%. Our results demonstrate that representation of profile-HMMs using a clustering-based approach can significantly accelerate data retrieval from profile-HMM databases.

  18. Database Description - fRNAdb | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available Affiliation: National Institute of Advanced Industrial Science and Technology (AIST) Journal Search: Creato...D89-92 External Links: Original website information Database maintenance site National Institute of Industrial Science and Technology

  19. FDA's Activities Supporting Regulatory Application of "Next Gen" Sequencing Technologies.

    Science.gov (United States)

    Wilson, Carolyn A; Simonyan, Vahan

    2014-01-01

    Applications of next-generation sequencing (NGS) technologies require availability and access to an information technology (IT) infrastructure and bioinformatics tools for large amounts of data storage and analyses. The U.S. Food and Drug Administration (FDA) anticipates that the use of NGS data to support regulatory submissions will continue to increase as the scientific and clinical communities become more familiar with the technologies and identify more ways to apply these advanced methods to support development and evaluation of new biomedical products. FDA laboratories are conducting research on different NGS platforms and developing the IT infrastructure and bioinformatics tools needed to enable regulatory evaluation of the technologies and the data sponsors will submit. A High-performance Integrated Virtual Environment, or HIVE, has been launched, and development and refinement continues as a collaborative effort between the FDA and George Washington University to provide the tools to support these needs. The use of a highly parallelized environment facilitated by use of distributed cloud storage and computation has resulted in a platform that is both rapid and responsive to changing scientific needs. The FDA plans to further develop in-house capacity in this area, while also supporting engagement by the external community, by sponsoring an open, public workshop to discuss NGS technologies and data formats standardization, and to promote the adoption of interoperability protocols in September 2014. Next-generation sequencing (NGS) technologies are enabling breakthroughs in how the biomedical community is developing and evaluating medical products. One example is the potential application of this method to the detection and identification of microbial contaminants in biologic products. In order for the U.S. Food and Drug Administration (FDA) to be able to evaluate the utility of this technology, we need to have the information technology infrastructure and

  20. TU-AB-204-00: CDRH/FDA Regulatory Processes and Device Science Activities

    International Nuclear Information System (INIS)

    2016-01-01

    The responsibilities of the Food and Drug Administration (FDA) have increased since the inception of the Food and Drugs Act in 1906. Medical devices first came under comprehensive regulation with the passage of the 1938 Food, Drug, and Cosmetic Act. In 1971 FDA also took on the responsibility for consumer protection against unnecessary exposure to radiation-emitting devices for home and occupational use. However it was not until 1976, under the Medical Device Regulation Act, that the FDA was responsible for the safety and effectiveness of medical devices. This session will be presented by the Division of Radiological Health (DRH) and the Division of Imaging, Diagnostics, and Software Reliability (DIDSR) from the Center for Devices and Radiological Health (CDRH) at the FDA. The symposium will discuss on how we protect and promote public health with a focus on medical physics applications organized into four areas: pre-market device review, post-market surveillance, device compliance, current regulatory research efforts and partnerships with other organizations. The pre-market session will summarize the pathways FDA uses to regulate the investigational use and commercialization of diagnostic imaging and radiation therapy medical devices in the US, highlighting resources available to assist investigators and manufacturers. The post-market session will explain the post-market surveillance and compliance activities FDA performs to monitor the safety and effectiveness of devices on the market. The third session will describe research efforts that support the regulatory mission of the Agency. An overview of our regulatory research portfolio to advance our understanding of medical physics and imaging technologies and approaches to their evaluation will be discussed. Lastly, mechanisms that FDA uses to seek public input and promote collaborations with professional, government, and international organizations, such as AAPM, International Electrotechnical Commission (IEC

  1. TU-AB-204-00: CDRH/FDA Regulatory Processes and Device Science Activities

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2016-06-15

    The responsibilities of the Food and Drug Administration (FDA) have increased since the inception of the Food and Drugs Act in 1906. Medical devices first came under comprehensive regulation with the passage of the 1938 Food, Drug, and Cosmetic Act. In 1971 FDA also took on the responsibility for consumer protection against unnecessary exposure to radiation-emitting devices for home and occupational use. However it was not until 1976, under the Medical Device Regulation Act, that the FDA was responsible for the safety and effectiveness of medical devices. This session will be presented by the Division of Radiological Health (DRH) and the Division of Imaging, Diagnostics, and Software Reliability (DIDSR) from the Center for Devices and Radiological Health (CDRH) at the FDA. The symposium will discuss on how we protect and promote public health with a focus on medical physics applications organized into four areas: pre-market device review, post-market surveillance, device compliance, current regulatory research efforts and partnerships with other organizations. The pre-market session will summarize the pathways FDA uses to regulate the investigational use and commercialization of diagnostic imaging and radiation therapy medical devices in the US, highlighting resources available to assist investigators and manufacturers. The post-market session will explain the post-market surveillance and compliance activities FDA performs to monitor the safety and effectiveness of devices on the market. The third session will describe research efforts that support the regulatory mission of the Agency. An overview of our regulatory research portfolio to advance our understanding of medical physics and imaging technologies and approaches to their evaluation will be discussed. Lastly, mechanisms that FDA uses to seek public input and promote collaborations with professional, government, and international organizations, such as AAPM, International Electrotechnical Commission (IEC

  2. Evidence behind FDA alerts for drugs with adverse cardiovascular effects: implications for clinical practice.

    Science.gov (United States)

    Rackham, Daniel M; C Herink, Megan; Stevens, Ian G; Cardoza, Natalie M; Singh, Harleen

    2014-01-01

    The U.S. Food and Drug Administration (FDA) periodically publishes Drug Safety Communications and Drug Alerts notifying health care practitioners and the general public of important information regarding drug therapies following FDA approval. These alerts can result in both positive and negative effects on patient care. Most clinical trials are not designed to detect long-term safety end points, and postmarketing surveillance along with patient reported events are often instrumental in signaling the potential harmful effect of a drug. Recently, many cardiovascular (CV) safety announcements have been released for FDA-approved drugs. Because a premature warning could discourage a much needed treatment or prompt a sudden discontinuation, it is essential to evaluate the evidence supporting these FDA alerts to provide effective patient care and to avoid unwarranted changes in therapy. Conversely, paying attention to these warnings in cases involving high-risk patients can prevent adverse effects and litigation. This article reviews the evidence behind recent FDA alerts for drugs with adverse CV effects and discusses the clinical practice implications. © 2013 Pharmacotherapy Publications, Inc.

  3. Content-Based Information Retrieval from Forensic Databases

    NARCIS (Netherlands)

    Geradts, Z.J.M.H.

    2002-01-01

    In forensic science, the number of image databases is growing rapidly. For this reason, it is necessary to have a proper procedure for searching in these images databases based on content. The use of image databases results in more solved crimes; furthermore, statistical information can be obtained

  4. FDA publishes checklist of Y2K high-risk devices.

    Science.gov (United States)

    1999-09-01

    Key points. The federal Food and Drug Administration (FDA) has developed a list of types of medical devices that have the potential for the most serious consequences for patients should they fail because of Y2K-related problems. This list of computer-controlled potentially high-risk devices can provide a guide to health care facilities regarding the types of devices that should receive priority in their assessment and remediation of medical devices. The list may change as the FDA receives comments on the types of devices included in the list.

  5. CAGE peaks - FANTOM5 | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data List Contact us FANTOM...E Data file File name: CAGE_peaks File URL: ftp://ftp.biosciencedbc.jp/archive/fantom... This Database Database Description Download License Update History of This Database Site Policy | Contact Us CAGE peaks - FANTOM5 | LSDB Archive ...

  6. Modelling antibody side chain conformations using heuristic database search.

    Science.gov (United States)

    Ritchie, D W; Kemp, G J

    1997-01-01

    We have developed a knowledge-based system which models the side chain conformations of residues in the variable domains of antibody Fv fragments. The system is written in Prolog and uses an object-oriented database of aligned antibody structures in conjunction with a side chain rotamer library. The antibody database provides 3-dimensional clusters of side chain conformations which can be copied en masse into the model structure. The object-oriented database architecture facilitates a navigational style of database access, necessary to assemble side chains clusters. Around 60% of the model is built using side chain clusters and this eliminates much of the combinatorial complexity associated with many other side chain placement algorithms. Construction and placement of side chain clusters is guided by a heuristic cost function based on a simple model of side chain packing interactions. Even with a simple model, we find that a large proportion of side chain conformations are modelled accurately. We expect our approach could be used with other homologous protein families, in addition to antibodies, both to improve the quality of model structures and to give a "smart start" to the side chain placement problem.

  7. High performance ZIF-8/6FDA-DAM mixed matrix membrane for propylene/propane separations

    KAUST Repository

    Zhang, Chen; Dai, Ying; Johnson, Justin R.; Karvan, Oguz; Koros, William J.

    2012-01-01

    We report significantly enhanced propylene/propane (C 3H 6/C 3H 8) selectivity in mixed matrix membranes fabricated using 6FDA-DAM polyimide and a zeolitic imidazolate framework (ZIF-8). Equilibrium isotherms and sorption kinetics of C 3H 6 and C 3H 8 at 35°C were studied on a 200nm commercially available ZIF-8 sample produced by BASF. Mixed matrix dense films were formed with 6FDA-DAM and 200nm BASF ZIF-8 particles. SEM imaging showed generally good adhesion between the ZIF-8 and 6FDA-DAM without the need for surface-treating ZIF-8. Pure gas permeation showed significantly enhanced mixed matrix ZIF-8/6FDA-DAM membrane C 3H 6/C 3H 8 separation performance over the pure 6FDA-DAM membrane performance. A C 3H 6 permeability of 56.2Barrer and C 3H 6/C 3H 8 ideal selectivity of 31.0 was found in ZIF-8/6FDA-DAM mixed matrix membrane with 48.0wt% ZIF-8 loading, which are 258% and 150% higher than the pure 6FDA-DAM membrane, respectively for permeability and selectivity. Permeation properties of C 3H 6 and C 3H 8 in ZIF-8 were back-calculated by the Maxwell model for composite permeability using pure gas permeation data, leading to a C 3H 6 permeability of 277Barrer and C 3H 6/C 3H 8 selectivity of 122. Mixed gas permeation also verified that selectivity enhancements were achievable in mixed gas environment by ZIF-8. © 2011 Elsevier B.V.

  8. High performance ZIF-8/6FDA-DAM mixed matrix membrane for propylene/propane separations

    KAUST Repository

    Zhang, Chen

    2012-02-01

    We report significantly enhanced propylene/propane (C 3H 6/C 3H 8) selectivity in mixed matrix membranes fabricated using 6FDA-DAM polyimide and a zeolitic imidazolate framework (ZIF-8). Equilibrium isotherms and sorption kinetics of C 3H 6 and C 3H 8 at 35°C were studied on a 200nm commercially available ZIF-8 sample produced by BASF. Mixed matrix dense films were formed with 6FDA-DAM and 200nm BASF ZIF-8 particles. SEM imaging showed generally good adhesion between the ZIF-8 and 6FDA-DAM without the need for surface-treating ZIF-8. Pure gas permeation showed significantly enhanced mixed matrix ZIF-8/6FDA-DAM membrane C 3H 6/C 3H 8 separation performance over the pure 6FDA-DAM membrane performance. A C 3H 6 permeability of 56.2Barrer and C 3H 6/C 3H 8 ideal selectivity of 31.0 was found in ZIF-8/6FDA-DAM mixed matrix membrane with 48.0wt% ZIF-8 loading, which are 258% and 150% higher than the pure 6FDA-DAM membrane, respectively for permeability and selectivity. Permeation properties of C 3H 6 and C 3H 8 in ZIF-8 were back-calculated by the Maxwell model for composite permeability using pure gas permeation data, leading to a C 3H 6 permeability of 277Barrer and C 3H 6/C 3H 8 selectivity of 122. Mixed gas permeation also verified that selectivity enhancements were achievable in mixed gas environment by ZIF-8. © 2011 Elsevier B.V.

  9. Main - KOME | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...ntents List of datasets Data file File name: kome_main.zip File URL: ftp://ftp.biosciencedbc.jp/archive/kome...ase Database Description Download License Update History of This Database Site Policy | Contact Us Main - KOME | LSDB Archive ...

  10. Combining history of medicine and library instruction: an innovative approach to teaching database searching to medical students.

    Science.gov (United States)

    Timm, Donna F; Jones, Dee; Woodson, Deidra; Cyrus, John W

    2012-01-01

    Library faculty members at the Health Sciences Library at the LSU Health Shreveport campus offer a database searching class for third-year medical students during their surgery rotation. For a number of years, students completed "ten-minute clinical challenges," but the instructors decided to replace the clinical challenges with innovative exercises using The Edwin Smith Surgical Papyrus to emphasize concepts learned. The Surgical Papyrus is an online resource that is part of the National Library of Medicine's "Turning the Pages" digital initiative. In addition, vintage surgical instruments and historic books are displayed in the classroom to enhance the learning experience.

  11. Possible use of fuzzy logic in database

    Directory of Open Access Journals (Sweden)

    Vaclav Bezdek

    2011-04-01

    Full Text Available The article deals with fuzzy logic and its possible use in database systems. At first fuzzy thinking style is shown on a simple example. Next the advantages of the fuzzy approach to database searching are considered on the database of used cars in the Czech Republic.

  12. BRC - MicrobeDB.jp | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...table). Data file File name: brc.tar.gz File URL: ftp://ftp.biosciencedbc.jp/archive/microbedb/LATEST/brc.ta...rains in JCM. About This Database Database Description Download License Update History of This Database Site Policy | Contact Us BRC - MicrobeDB.jp | LSDB Archive ...

  13. SRA - MicrobeDB.jp | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...e following table). Data file File name: sra.tar.gz File URL: ftp://ftp.biosciencedbc.jp/archive/microbedb/L...t This Database Database Description Download License Update History of This Database Site Policy | Contact Us SRA - MicrobeDB.jp | LSDB Archive ...

  14. A comparative study of six European databases of medically oriented Web resources.

    Science.gov (United States)

    Abad García, Francisca; González Teruel, Aurora; Bayo Calduch, Patricia; de Ramón Frias, Rosa; Castillo Blasco, Lourdes

    2005-10-01

    The paper describes six European medically oriented databases of Web resources, pertaining to five quality-controlled subject gateways, and compares their performance. The characteristics, coverage, procedure for selecting Web resources, record structure, searching possibilities, and existence of user assistance were described for each database. Performance indicators for each database were obtained by means of searches carried out using the key words, "myocardial infarction." Most of the databases originated in the 1990s in an academic or library context and include all types of Web resources of an international nature. Five databases use Medical Subject Headings. The number of fields per record varies between three and nineteen. The language of the search interfaces is mostly English, and some of them allow searches in other languages. In some databases, the search can be extended to Pubmed. Organizing Medical Networked Information, Catalogue et Index des Sites Médicaux Francophones, and Diseases, Disorders and Related Topics produced the best results. The usefulness of these databases as quick reference resources is clear. In addition, their lack of content overlap means that, for the user, they complement each other. Their continued survival faces three challenges: the instability of the Internet, maintenance costs, and lack of use in spite of their potential usefulness.

  15. Dose Matters: FDA's Guidance on Children's X-rays

    Science.gov (United States)

    ... Consumer Updates Dose Matters: FDA's Guidance on Children's X-rays Share Tweet Linkedin Pin it More sharing options ... exposure during medical procedures. The level of ionizing radiation from X-ray imaging is generally very low, but can ...

  16. Search Engines for Tomorrow's Scholars

    Science.gov (United States)

    Fagan, Jody Condit

    2011-01-01

    Today's scholars face an outstanding array of choices when choosing search tools: Google Scholar, discipline-specific abstracts and index databases, library discovery tools, and more recently, Microsoft's re-launch of their academic search tool, now dubbed Microsoft Academic Search. What are these tools' strengths for the emerging needs of…

  17. Enabling Searches on Wavelengths in a Hyperspectral Indices Database

    Science.gov (United States)

    Piñuela, F.; Cerra, D.; Müller, R.

    2017-10-01

    Spectral indices derived from hyperspectral reflectance measurements are powerful tools to estimate physical parameters in a non-destructive and precise way for several fields of applications, among others vegetation health analysis, coastal and deep water constituents, geology, and atmosphere composition. In the last years, several micro-hyperspectral sensors have appeared, with both full-frame and push-broom acquisition technologies, while in the near future several hyperspectral spaceborne missions are planned to be launched. This is fostering the use of hyperspectral data in basic and applied research causing a large number of spectral indices to be defined and used in various applications. Ad hoc search engines are therefore needed to retrieve the most appropriate indices for a given application. In traditional systems, query input parameters are limited to alphanumeric strings, while characteristics such as spectral range/ bandwidth are not used in any existing search engine. Such information would be relevant, as it enables an inverse type of search: given the spectral capabilities of a given sensor or a specific spectral band, find all indices which can be derived from it. This paper describes a tool which enables a search as described above, by using the central wavelength or spectral range used by a given index as a search parameter. This offers the ability to manage numeric wavelength ranges in order to select indices which work at best in a given set of wavelengths or wavelength ranges.

  18. DB-PABP: a database of polyanion-binding proteins.

    Science.gov (United States)

    Fang, Jianwen; Dong, Yinghua; Salamat-Miller, Nazila; Middaugh, C Russell

    2008-01-01

    The interactions between polyanions (PAs) and polyanion-binding proteins (PABPs) have been found to play significant roles in many essential biological processes including intracellular organization, transport and protein folding. Furthermore, many neurodegenerative disease-related proteins are PABPs. Thus, a better understanding of PA/PABP interactions may not only enhance our understandings of biological systems but also provide new clues to these deadly diseases. The literature in this field is widely scattered, suggesting the need for a comprehensive and searchable database of PABPs. The DB-PABP is a comprehensive, manually curated and searchable database of experimentally characterized PABPs. It is freely available and can be accessed online at http://pabp.bcf.ku.edu/DB_PABP/. The DB-PABP was implemented as a MySQL relational database. An interactive web interface was created using Java Server Pages (JSP). The search page of the database is organized into a main search form and a section for utilities. The main search form enables custom searches via four menus: protein names, polyanion names, the source species of the proteins and the methods used to discover the interactions. Available utilities include a commonality matrix, a function of listing PABPs by the number of interacting polyanions and a string search for author surnames. The DB-PABP is maintained at the University of Kansas. We encourage users to provide feedback and submit new data and references.

  19. Evidence-based librarianship: searching for the needed EBL evidence.

    Science.gov (United States)

    Eldredge, J D

    2000-01-01

    This paper discusses the challenges of finding evidence needed to implement Evidence-Based Librarianship (EBL). Focusing first on database coverage for three health sciences librarianship journals, the article examines the information contents of different databases. Strategies are needed to search for relevant evidence in the library literature via these databases, and the problems associated with searching the grey literature of librarianship. Database coverage, plausible search strategies, and the grey literature of library science all pose challenges to finding the needed research evidence for practicing EBL. Health sciences librarians need to ensure that systems are designed that can track and provide access to needed research evidence to support Evidence-Based Librarianship (EBL).

  20. Single Cigarette Sales: State Differences in FDA Advertising and Labeling Violations, 2014, United States.

    Science.gov (United States)

    Baker, Hannah M; Lee, Joseph G L; Ranney, Leah M; Goldstein, Adam O

    2016-02-01

    Single cigarettes, which are sold without warning labels and often evade taxes, can serve as a gateway for youth smoking. The Family Smoking Prevention and Tobacco Control Act of 2009 gives the US Food and Drug Administration (FDA) authority to regulate the manufacture, distribution, and marketing of tobacco products, including prohibiting the sale of single cigarettes. To enforce these regulations, the FDA conducted over 335,661 inspections between 2010 and September 30, 2014, and allocated over $115 million toward state inspections contracts. To examine differences in single cigarette violations across states and determine if likely correlates of single cigarette sales predict single cigarette violations at the state level. Cross-sectional study of publicly available FDA warning letters from January 1 to July 31, 2014. All 50 states and the District of Columbia. Tobacco retailer inspections conducted by FDA (n = 33 543). State cigarette tax, youth smoking prevalence, poverty, and tobacco production. State proportion of FDA warning letters issued for single cigarette violations. There are striking differences in the number of single cigarette violations found by state, with 38 states producing no warning letters for selling single cigarettes even as state policymakers developed legislation to address retailer sales of single cigarettes. The state proportion of warning letters issued for single cigarettes is not predicted by state cigarette tax, youth smoking, poverty, or tobacco production, P = .12. Substantial, unexplained variation exists in violations of single cigarette sales among states. These data suggest the possibility of differences in implementation of FDA inspections and the need for stronger quality monitoring processes across states implementing FDA inspections. © The Author 2015. Published by Oxford University Press on behalf of the Society for Research on Nicotine and Tobacco. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  1. Information Retrieval in Telemedicine: a Comparative Study on Bibliographic Databases.

    Science.gov (United States)

    Ahmadi, Maryam; Sarabi, Roghayeh Ershad; Orak, Roohangiz Jamshidi; Bahaadinbeigy, Kambiz

    2015-06-01

    The first step in each systematic review is selection of the most valid database that can provide the highest number of relevant references. This study was carried out to determine the most suitable database for information retrieval in telemedicine field. Cinhal, PubMed, Web of Science and Scopus databases were searched for telemedicine matched with Education, cost benefit and patient satisfaction. After analysis of the obtained results, the accuracy coefficient, sensitivity, uniqueness and overlap of databases were calculated. The studied databases differed in the number of retrieved articles. PubMed was identified as the most suitable database for retrieving information on the selected topics with the accuracy and sensitivity ratios of 50.7% and 61.4% respectively. The uniqueness percent of retrieved articles ranged from 38% for Pubmed to 3.0% for Cinhal. The highest overlap rate (18.6%) was found between PubMed and Web of Science. Less than 1% of articles have been indexed in all searched databases. PubMed is suggested as the most suitable database for starting search in telemedicine and after PubMed, Scopus and Web of Science can retrieve about 90% of the relevant articles.

  2. Movie collection - TogoTV | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...ols. Data file File name: movie File URL: ftp://ftp.biosciencedbc.jp/archive/togotv/movie/ File size: 200 GB...ata entries 1169 entries - About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Movie collection - TogoTV | LSDB Archive ...

  3. PubMed searches: overview and strategies for clinicians.

    Science.gov (United States)

    Lindsey, Wesley T; Olin, Bernie R

    2013-04-01

    PubMed is a biomedical and life sciences database maintained by a division of the National Library of Medicine known as the National Center for Biotechnology Information (NCBI). It is a large resource with more than 5600 journals indexed and greater than 22 million total citations. Searches conducted in PubMed provide references that are more specific for the intended topic compared with other popular search engines. Effective PubMed searches allow the clinician to remain current on the latest clinical trials, systematic reviews, and practice guidelines. PubMed continues to evolve by allowing users to create a customized experience through the My NCBI portal, new arrangements and options in search filters, and supporting scholarly projects through exportation of citations to reference managing software. Prepackaged search options available in the Clinical Queries feature also allow users to efficiently search for clinical literature. PubMed also provides information regarding the source journals themselves through the Journals in NCBI Databases link. This article provides an overview of the PubMed database's structure and features as well as strategies for conducting an effective search.

  4. Database-independent, database-dependent, and extended interpretation of peptide mass spectra in VEMS V2.0

    DEFF Research Database (Denmark)

    Matthiesen, Rune; Bunkenborg, Jakob; Stensballe, Allan

    2004-01-01

    , and generation of protein and peptide databases. VEMS V2.0 has been developed into a fast tool for combining database-independent and -dependent protein assignments in an extended analysis of MS/MS-peptide data. MS or MS/MS data can be directly recalibrated after the first search by fitting the data to the best...... search result using polynomial equations. The score function is an improvement of known scoring algorithms and can be adapted for any MS instrument type. In addition, VEMS offers a novel statistical model for evaluating the significance of the protein assignment. The novel features are illustrated...

  5. Main - AT Atlas | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ... name: at_atlas_en.zip File URL: ftp://ftp.biosciencedbc.jp/archive/at_atlas/LATE... Database Description Download License Update History of This Database Site Policy | Contact Us Main - AT Atlas | LSDB Archive ...

  6. Protein (Cyanobacteria) - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available ut This Database Database Description Download License Update History of This Database Site Policy | Contact Us Protein (Cyanobacteria) - PGDBj - Ortholog DB | LSDB Archive ... ...List Contact us PGDBj - Ortholog DB Protein (Cyanobacteria) Data detail Data name Protein (Cyanobacteria) DO...switchLanguage; BLAST Search Image Search Home About Archive Update History Data

  7. The CAPEC Database

    DEFF Research Database (Denmark)

    Nielsen, Thomas Lund; Abildskov, Jens; Harper, Peter Mathias

    2001-01-01

    in the compound. This classification makes the CAPEC database a very useful tool, for example, in the development of new property models, since properties of chemically similar compounds are easily obtained. A program with efficient search and retrieval functions of properties has been developed.......The Computer-Aided Process Engineering Center (CAPEC) database of measured data was established with the aim to promote greater data exchange in the chemical engineering community. The target properties are pure component properties, mixture properties, and special drug solubility data....... The database divides pure component properties into primary, secondary, and functional properties. Mixture properties are categorized in terms of the number of components in the mixture and the number of phases present. The compounds in the database have been classified on the basis of the functional groups...

  8. The Lung Image Database Consortium (LIDC) and Image Database Resource Initiative (IDRI): A Completed Reference Database of Lung Nodules on CT Scans

    International Nuclear Information System (INIS)

    2011-01-01

    Purpose: The development of computer-aided diagnostic (CAD) methods for lung nodule detection, classification, and quantitative assessment can be facilitated through a well-characterized repository of computed tomography (CT) scans. The Lung Image Database Consortium (LIDC) and Image Database Resource Initiative (IDRI) completed such a database, establishing a publicly available reference for the medical imaging research community. Initiated by the National Cancer Institute (NCI), further advanced by the Foundation for the National Institutes of Health (FNIH), and accompanied by the Food and Drug Administration (FDA) through active participation, this public-private partnership demonstrates the success of a consortium founded on a consensus-based process. Methods: Seven academic centers and eight medical imaging companies collaborated to identify, address, and resolve challenging organizational, technical, and clinical issues to provide a solid foundation for a robust database. The LIDC/IDRI Database contains 1018 cases, each of which includes images from a clinical thoracic CT scan and an associated XML file that records the results of a two-phase image annotation process performed by four experienced thoracic radiologists. In the initial blinded-read phase, each radiologist independently reviewed each CT scan and marked lesions belonging to one of three categories (''nodule≥3 mm,''''nodule<3 mm,'' and ''non-nodule≥3 mm''). In the subsequent unblinded-read phase, each radiologist independently reviewed their own marks along with the anonymized marks of the three other radiologists to render a final opinion. The goal of this process was to identify as completely as possible all lung nodules in each CT scan without requiring forced consensus. Results: The Database contains 7371 lesions marked ''nodule'' by at least one radiologist. 2669 of these lesions were marked ''nodule≥3 mm'' by at least one radiologist, of which 928 (34.7%) received such marks from all

  9. Medicare covers the majority of FDA-approved devices and Part B drugs, but restrictions and discrepancies remain.

    Science.gov (United States)

    Chambers, James D; May, Katherine E; Neumann, Peter J

    2013-06-01

    The Food and Drug Administration (FDA) and Medicare use different standards to determine, first, whether a new drug or medical device can be marketed to the public and, second, if the federal health insurance program will pay for use of the drug or device. This discrepancy creates hurdles and uncertainty for drug and device manufacturers. We analyzed discrepancies between FDA approval and Medicare national coverage determinations for sixty-nine devices and Part B drugs approved during 1999-2011. We found that Medicare covered FDA-approved drugs or devices 80 percent of the time. However, Medicare often added conditions beyond FDA approval, particularly for devices and most often restricting coverage to patients with the most severe disease. In some instances, Medicare was less restrictive than the FDA. Our findings highlight the importance for drug and device makers of anticipating Medicare's needs when conducting clinical studies to support their products. Our findings also provide important insights for the FDA's and Medicare's pilot parallel review program.

  10. Multilingual Federated Searching Across Heterogeneous Collections.

    Science.gov (United States)

    Powell, James; Fox, Edward A.

    1998-01-01

    Describes a scalable system for searching heterogeneous multilingual collections on the World Wide Web. Details Searchable Database Markup Language (SearchDB-ML) for describing the characteristics of a search engine and its interface, and a protocol for requesting word translations between languages. (Author)

  11. Quality assessment of digital annotated ECG data from clinical trials by the FDA ECG Warehouse.

    Science.gov (United States)

    Sarapa, Nenad

    2007-09-01

    The FDA mandates that digital electrocardiograms (ECGs) from 'thorough' QTc trials be submitted into the ECG Warehouse in Health Level 7 extended markup language format with annotated onset and offset points of waveforms. The FDA did not disclose the exact Warehouse metrics and minimal acceptable quality standards. The author describes the Warehouse scoring algorithms and metrics used by FDA, points out ways to improve FDA review and suggests Warehouse benefits for pharmaceutical sponsors. The Warehouse ranks individual ECGs according to their score for each quality metric and produces histogram distributions with Warehouse-specific thresholds that identify ECGs of questionable quality. Automatic Warehouse algorithms assess the quality of QT annotation and duration of manual QT measurement by the central ECG laboratory.

  12. An Improved Forensic Science Information Search.

    Science.gov (United States)

    Teitelbaum, J

    2015-01-01

    Although thousands of search engines and databases are available online, finding answers to specific forensic science questions can be a challenge even to experienced Internet users. Because there is no central repository for forensic science information, and because of the sheer number of disciplines under the forensic science umbrella, forensic scientists are often unable to locate material that is relevant to their needs. The author contends that using six publicly accessible search engines and databases can produce high-quality search results. The six resources are Google, PubMed, Google Scholar, Google Books, WorldCat, and the National Criminal Justice Reference Service. Carefully selected keywords and keyword combinations, designating a keyword phrase so that the search engine will search on the phrase and not individual keywords, and prompting search engines to retrieve PDF files are among the techniques discussed. Copyright © 2015 Central Police University.

  13. Preparing College Students To Search Full-Text Databases: Is Instruction Necessary?

    Science.gov (United States)

    Riley, Cheryl; Wales, Barbara

    Full-text databases allow Central Missouri State University's clients to access some of the serials that libraries have had to cancel due to escalating subscription costs; EbscoHost, the subject of this study, is one such database. The database is available free to all Missouri residents. A survey was designed consisting of 21 questions intended…

  14. No sisyphean task: how the FDA can regulate electronic cigarettes.

    Science.gov (United States)

    Paradise, Jordan

    2013-01-01

    The adverse effects of smoking have fostered a natural market for smoking cessation and smoking reduction products. Smokers attempting to quit or reduce consumption have tried everything: "low" or "light" cigarettes; nicotine-infused chewing gum, lozenges, and lollipops; dermal patches; and even hypnosis. The latest craze in the quest to find a safer source of nicotine is the electronic cigarette. Electronic cigarettes (e-cigarettes) have swept the market, reaching a rapidly expanding international consumer base. Boasting nicotine delivery and the tactile feel of a traditional cigarette without the dozens of other chemical constituents that contribute to carcinogenicity, e-cigarettes are often portrayed as less risky, as a smoking reduction or even a complete smoking cessation product, and perhaps most troubling for its appeal to youth, as a flavorful, trendy, and convenient accessory. The sensationalism associated with e-cigarettes has spurred outcry from health and medical professional groups, as well as the Food and Drug Administration (FDA), because of the unknown effects on public health. Inhabiting a realm of products deemed "tobacco products" under recent 2009 legislation, e-cigarettes pose new challenges to FDA regulation because of their novel method of nicotine delivery, various mechanical and electrical parts, and nearly nonexistent safety data. Consumer use, marketing and promotional claims, and technological characteristics of e-cigarettes have also raised decades old questions of when the FDA can assert authority over products as drugs or medical devices. Recent case law restricting FDA enforcement efforts against e-cigarettes further confounds the distinction among drugs and medical devices, emerging e-cigarette products, and traditional tobacco products such as cigarettes, cigars, and smokeless tobacco. This Article investigates the e-cigarette phenomenon in the wake of the recently enacted Family Smoking Prevention and Tobacco Control Act of 2009

  15. Analysis list - ChIP-Atlas | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...://ftp.biosciencedbc.jp/archive/chip-atlas/LATEST/chip_atlas_analysis_list.zip File size: 44.8 KB Simple sea...e class. About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Analysis list - ChIP-Atlas | LSDB Archive ...

  16. The North Carolina State University Libraries Search Experience: Usability Testing Tabbed Search Interfaces for Academic Libraries

    Science.gov (United States)

    Teague-Rector, Susan; Ballard, Angela; Pauley, Susan K.

    2011-01-01

    Creating a learnable, effective, and user-friendly library Web site hinges on providing easy access to search. Designing a search interface for academic libraries can be particularly challenging given the complexity and range of searchable library collections, such as bibliographic databases, electronic journals, and article search silos. Library…

  17. Hepatitis B infection reported with cancer chemotherapy: analyzing the US FDA Adverse Event Reporting System.

    Science.gov (United States)

    Sanagawa, Akimasa; Hotta, Yuji; Kataoka, Tomoya; Maeda, Yasuhiro; Kondo, Masahiro; Kawade, Yoshihiro; Ogawa, Yoshihiro; Nishikawa, Ryohei; Tohkin, Masahiro; Kimura, Kazunori

    2018-04-16

    We conducted data mining using the US Food and Drug Administration (FDA) Adverse Event Reporting System (FAERS) database on spontaneously reported adverse events to evaluate the association between anticancer drug therapy and hepatitis B infection. Reports of hepatitis B infection were retrieved from the FAERS database. The reporting odds ratio (ROR) was used to estimate the association between hepatitis B infection and various anticancer agents and drug combinations. We detected statistically significant risk signals of hepatitis B for 33 of 64 anticancer agents by ROR (26 cytotoxicity drugs and seven molecular-targeted drugs). We focused on molecular-targeted drugs and assessed the risk of hepatitis B from specific anticancer drug combinations. The frequency of hepatitis B infection was significantly high for drugs such as rituximab, bortezomib, imatinib, and everolimus. The addition of cyclophosphamide, doxorubicin, and fludarabine to drug combinations additively enhanced the frequency of hepatitis B infection. There were no reports on hepatitis B infection associated with trastuzumab or azacitidine monotherapy. However, trastuzumab-containing regimens (e.g., combinations with docetaxel or paclitaxel) were correlated with the incidence of hepatitis B infection, similar to azacitidine monotherapy. Our findings suggest that the concomitant use of anticancer drugs, such as trastuzumab, taxane, and azacitidine, may contribute to the risk of hepatitis B infection. The unique signals detected from the public database might provide clues to eliminate the threat of HBV in oncology. © 2018 The Authors. Cancer Medicine published by John Wiley & Sons Ltd.

  18. A student's guide to searching the literature using online databases

    Science.gov (United States)

    Miller, Casey W.; Belyea, Dustin; Chabot, Michelle; Messina, Troy

    2012-02-01

    A method is described to empower students to efficiently perform general and specific literature searches using online resources [Miller et al., Am. J. Phys. 77, 1112 (2009)]. The method was tested on multiple groups, including undergraduate and graduate students with varying backgrounds in scientific literature searches. Students involved in this study showed marked improvement in their awareness of how and where to find scientific information. Repeated exposure to literature searching methods appears worthwhile, starting early in the undergraduate career, and even in graduate school orientation.

  19. Healthcare professionals and pharmacovigilance of pediatric adverse drug reactions: a 5-year analysis of Adverse Events Reporting System database of the Food and Drug Administration.

    Science.gov (United States)

    Bigi, Caterina; Tuccori, Marco; Bocci, Guido

    2017-02-17

    To analyze the Adverse Events Reporting System (AERS) database of the Food and Drug Administration (FDA), investigating the characteristics of pediatric adverse drug reactions (ADRs) and describing the effective participation of healthcare professionals in the reporting activity. Reports of ADRs were obtained from the FDA website. Only ADRs in pediatric subjects (divided by age, by country and by professional category) were included into the analysis. The drugs suspected as primary cause of the ADRs in pediatric subjects and their principal anatomic group according to the Anatomical Therapeutic Chemical classification system were considered. To classify the ADRs, the Medical Dictionary for Regularity Activities terminology was adopted. Between 2008 and 2012, FDA collected 113,077 ADRs in pediatric patients. Of the total pediatric ADR reports, those performed by medical doctors were 32%, followed by consumers (26%) and healthcare professionals (25%). Most of the ADR reports were related to the adolescent group (39%). Healthcare professionals resulted the category with the highest rate of ADR reports in neonates and infants. Drugs acting on nervous system and antineoplastic/immunomodulating agents were the most involved the pediatric ADR reports. Pyrexia, convulsion, vomiting and accidental overdose were the reactions more reported both from healthcare professionals and medical doctors. The present study describes the pediatric ADR reports of the FDA database through healthcare professional's perspective, describing the various aspects of pediatric pharmacovigilance.

  20. Beyond MEDLINE for literature searches.

    Science.gov (United States)

    Conn, Vicki S; Isaramalai, Sang-arun; Rath, Sabyasachi; Jantarakupt, Peeranuch; Wadhawan, Rohini; Dash, Yashodhara

    2003-01-01

    To describe strategies for a comprehensive literature search. MEDLINE searches result in limited numbers of studies that are often biased toward statistically significant findings. Diversified search strategies are needed. Empirical evidence about the recall and precision of diverse search strategies is presented. Challenges and strengths of each search strategy are identified. Search strategies vary in recall and precision. Often sensitivity and specificity are inversely related. Valuable search strategies include examination of multiple diverse computerized databases, ancestry searches, citation index searches, examination of research registries, journal hand searching, contact with the "invisible college," examination of abstracts, Internet searches, and contact with sources of synthesized information. Extending searches beyond MEDLINE enables researchers to conduct more systematic comprehensive searches.

  1. Could FDA approval of pre-exposure prophylaxis make a difference? A qualitative study of PrEP acceptability and FDA perceptions among men who have sex with men

    OpenAIRE

    Underhill, Kristen; Morrow, Kathleen M.; Operario, Don; Mayer, Kenneth H.

    2014-01-01

    The FDA has approved tenofovir-emtricitabine for use as HIV pre-exposure prophylaxis, but it is unknown how approval may affect PrEP acceptability among US men who have sex with men. We conducted 8 focus groups among 38 Rhode Island MSM, including 3 groups among 16 male sex workers and 5 groups among 22 men in the general MSM community. Participants reported wide-ranging beliefs regarding consequences and meanings of FDA approval. Some participants would not use PrEP without approval, while o...

  2. U.S. FDA Approval Summary: Nivolumab for Treatment of Unresectable or Metastatic Melanoma Following Progression on Ipilimumab.

    Science.gov (United States)

    Hazarika, Maitreyee; Chuk, Meredith K; Theoret, Marc R; Mushti, Sirisha; He, Kun; Weis, Shawna L; Putman, Alexander H; Helms, Whitney S; Cao, Xianhua; Li, Hongshan; Zhao, Hong; Zhao, Liang; Welch, Joel; Graham, Laurie; Libeg, Meredith; Sridhara, Rajeshwari; Keegan, Patricia; Pazdur, Richard

    2017-07-15

    On December 22, 2014, the FDA granted accelerated approval to nivolumab (OPDIVO; Bristol-Myers Squibb) for the treatment of patients with unresectable or metastatic melanoma and disease progression following ipilimumab and, if BRAF V600 mutation positive, a BRAF inhibitor. Approval was based on a clinically meaningful, durable objective response rate (ORR) in a non-comparative analysis of 120 patients who received 3 mg/kg of nivolumab intravenously every 2 weeks with at least 6-month follow-up in an ongoing, randomized, open-label, active-controlled clinical trial. The ORR as assessed by a blinded independent review committee per RECIST v1.1 was 31.7% (95% confidence interval, 23.5-40.8). Ongoing responses were observed in 87% of responding patients, ranging from 2.6+ to 10+ months. In 13 patients, the response duration was 6 months or longer. The risks of nivolumab, including clinically significant immune-mediated adverse reactions (imARs), were assessed in 268 patients who received at least one dose of nivolumab. The FDA review considered whether the ORR and durations of responses were reasonably likely to predict clinical benefit, the adequacy of the safety database, and systematic approaches to the identification, description, and patient management for imARs in product labeling. Clin Cancer Res; 23(14); 3484-8. ©2017 AACR . ©2017 American Association for Cancer Research.

  3. Cluster (Viridiplantae) - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available 0”. This cluster ID is uniquely-assigned by the PGDBj Ortholog Database. Cluster size Number of proteins aff...r About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Cluster (Viridiplantae) - PGDBj - Ortholog DB | LSDB Archive ... ...List Contact us PGDBj - Ortholog DB Cluster (Viridiplantae) Data detail Data name Cluster (Viridiplantae) DO...switchLanguage; BLAST Search Image Search Home About Archive Update History Data

  4. Cluster (Cyanobacteria) - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available 3090”. This cluster ID is uniquely-assigned by the PGDBj Ortholog Database. Cluster size Number of proteins ...ster About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Cluster (Cyanobacteria) - PGDBj - Ortholog DB | LSDB Archive ... ...List Contact us PGDBj - Ortholog DB Cluster (Cyanobacteria) Data detail Data name Cluster (Cyanobacteria) DO...switchLanguage; BLAST Search Image Search Home About Archive Update History Data

  5. Citation Searching: Search Smarter & Find More

    Science.gov (United States)

    Hammond, Chelsea C.; Brown, Stephanie Willen

    2008-01-01

    The staff at University of Connecticut are participating in Elsevier's Student Ambassador Program (SAmP) in which graduate students train their peers on "citation searching" research using Scopus and Web of Science, two tremendous citation databases. They are in the fourth semester of these training programs, and they are wildly successful: They…

  6. PREIMS - AT Atlas | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...Targeted Proteins Research Program (TPRP). Data file File name: at_atlas_preims.zip File URL: ftp://ftp.biosciencedbc.jp/archiv...base Database Description Download License Update History of This Database Site Policy | Contact Us PREIMS - AT Atlas | LSDB Archive ...

  7. Mobile object retrieval in server-based image databases

    Science.gov (United States)

    Manger, D.; Pagel, F.; Widak, H.

    2013-05-01

    The increasing number of mobile phones equipped with powerful cameras leads to huge collections of user-generated images. To utilize the information of the images on site, image retrieval systems are becoming more and more popular to search for similar objects in an own image database. As the computational performance and the memory capacity of mobile devices are constantly increasing, this search can often be performed on the device itself. This is feasible, for example, if the images are represented with global image features or if the search is done using EXIF or textual metadata. However, for larger image databases, if multiple users are meant to contribute to a growing image database or if powerful content-based image retrieval methods with local features are required, a server-based image retrieval backend is needed. In this work, we present a content-based image retrieval system with a client server architecture working with local features. On the server side, the scalability to large image databases is addressed with the popular bag-of-word model with state-of-the-art extensions. The client end of the system focuses on a lightweight user interface presenting the most similar images of the database highlighting the visual information which is common with the query image. Additionally, new images can be added to the database making it a powerful and interactive tool for mobile contentbased image retrieval.

  8. Customizable orthopaedic oncology implants: one institution's experience with meeting current IRB and FDA requirements.

    Science.gov (United States)

    Willis, Alexander R; Ippolito, Joseph A; Patterson, Francis R; Benevenia, Joseph; Beebe, Kathleen S

    2016-01-01

    Customizable orthopaedic implants are often needed for patients with primary malignant bone tumors due to unique anatomy or complex mechanical problems. Currently, obtaining customizable orthopaedic implants for orthopaedic oncology patients can be an arduous task involving submitting approval requests to the Institutional Review Board (IRB) and the Food and Drug Administration (FDA). There is great potential for the delay of a patient's surgery and unnecessary paperwork if the submission pathways are misunderstood or a streamlined protocol is not in place. The objective of this study was to review the existing FDA custom implant approval pathways and to determine whether this process was improved with an institutional protocol. An institutional protocol for obtaining IRB and FDA approval for customizable orthopaedic implants was established with the IRB at our institution in 2013. This protocol was approved by the IRB, such that new patients only require submission of a modification to the existing protocol with individualized patient information. During the two-year period of 2013-2014, eight patients were retrospectively identified as having required customizable implants for various orthopaedic oncology surgeries. The dates of request for IRB approval, request for FDA approval, and total time to surgery were recorded, along with the specific pathway utilized for FDA approval. The average patient age was 12 years old (7-21 years old). The average time to IRB approval of a modification to the pre-approved protocol was 14 days (7-21 days). Average time to FDA approval after submission of the IRB approval to the manufacturer was 12.5 days (7-19 days). FDA approval was obtained for all implants as compassionate use requests in accordance with Section 561 of the Federal Food Drug and Cosmetic Act's expanded access provisions. Establishment of an institutional protocol with pre-approval by the IRB can expedite the otherwise time-consuming and complicated

  9. ElasticSearch server

    CERN Document Server

    Rogozinski, Marek

    2014-01-01

    This book is a detailed, practical, hands-on guide packed with real-life scenarios and examples which will show you how to implement an ElasticSearch search engine on your own websites.If you are a web developer or a user who wants to learn more about ElasticSearch, then this is the book for you. You do not need to know anything about ElastiSeach, Java, or Apache Lucene in order to use this book, though basic knowledge about databases and queries is required.

  10. An ontology-based search engine for protein-protein interactions.

    Science.gov (United States)

    Park, Byungkyu; Han, Kyungsook

    2010-01-18

    Keyword matching or ID matching is the most common searching method in a large database of protein-protein interactions. They are purely syntactic methods, and retrieve the records in the database that contain a keyword or ID specified in a query. Such syntactic search methods often retrieve too few search results or no results despite many potential matches present in the database. We have developed a new method for representing protein-protein interactions and the Gene Ontology (GO) using modified Gödel numbers. This representation is hidden from users but enables a search engine using the representation to efficiently search protein-protein interactions in a biologically meaningful way. Given a query protein with optional search conditions expressed in one or more GO terms, the search engine finds all the interaction partners of the query protein by unique prime factorization of the modified Gödel numbers representing the query protein and the search conditions. Representing the biological relations of proteins and their GO annotations by modified Gödel numbers makes a search engine efficiently find all protein-protein interactions by prime factorization of the numbers. Keyword matching or ID matching search methods often miss the interactions involving a protein that has no explicit annotations matching the search condition, but our search engine retrieves such interactions as well if they satisfy the search condition with a more specific term in the ontology.

  11. Changes in the utilization of osteoporosis drugs after the 2010 FDA bisphosphonate drug safety communication

    Directory of Open Access Journals (Sweden)

    Bander Balkhi

    2018-02-01

    Conclusions: The 2010 FDA bisphosphonates safety communication appeared to have influenced Osteoporosis utilization in Medicaid recipients. The 2010 FDA bisphosphonates safety communication was associated with a significant reduction in the utilization of bisphosphonates in the Medicaid program.

  12. Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology

    International Nuclear Information System (INIS)

    Shen Yang; Bax, Ad

    2007-01-01

    Chemical shifts of nuclei in or attached to a protein backbone are exquisitely sensitive to their local environment. A computer program, SPARTA, is described that uses this correlation with local structure to predict protein backbone chemical shifts, given an input three-dimensional structure, by searching a newly generated database for triplets of adjacent residues that provide the best match in φ/ψ/χ 1 torsion angles and sequence similarity to the query triplet of interest. The database contains 15 N, 1 H N , 1 H α , 13 C α , 13 C β and 13 C' chemical shifts for 200 proteins for which a high resolution X-ray (≤2.4 A) structure is available. The relative importance of the weighting factors for the φ/ψ/χ 1 angles and sequence similarity was optimized empirically. The weighted, average secondary shifts of the central residues in the 20 best-matching triplets, after inclusion of nearest neighbor, ring current, and hydrogen bonding effects, are used to predict chemical shifts for the protein of known structure. Validation shows good agreement between the SPARTA-predicted and experimental shifts, with standard deviations of 2.52, 0.51, 0.27, 0.98, 1.07 and 1.08 ppm for 15 N, 1 H N , 1 H α , 13 C α , 13 C β and 13 C', respectively, including outliers

  13. SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters

    Directory of Open Access Journals (Sweden)

    Lefkowitz Elliot J

    2004-10-01

    Full Text Available Abstract Background Large-scale sequence comparison is a powerful tool for biological inference in modern molecular biology. Comparing new sequences to those in annotated databases is a useful source of functional and structural information about these sequences. Using software such as the basic local alignment search tool (BLAST or HMMPFAM to identify statistically significant matches between newly sequenced segments of genetic material and those in databases is an important task for most molecular biologists. Searching algorithms are intrinsically slow and data-intensive, especially in light of the rapid growth of biological sequence databases due to the emergence of high throughput DNA sequencing techniques. Thus, traditional bioinformatics tools are impractical on PCs and even on dedicated UNIX servers. To take advantage of larger databases and more reliable methods, high performance computation becomes necessary. Results We describe the implementation of SS-Wrapper (Similarity Search Wrapper, a package of wrapper applications that can parallelize similarity search applications on a Linux cluster. Our wrapper utilizes a query segmentation-search (QS-search approach to parallelize sequence database search applications. It takes into consideration load balancing between each node on the cluster to maximize resource usage. QS-search is designed to wrap many different search tools, such as BLAST and HMMPFAM using the same interface. This implementation does not alter the original program, so newly obtained programs and program updates should be accommodated easily. Benchmark experiments using QS-search to optimize BLAST and HMMPFAM showed that QS-search accelerated the performance of these programs almost linearly in proportion to the number of CPUs used. We have also implemented a wrapper that utilizes a database segmentation approach (DS-BLAST that provides a complementary solution for BLAST searches when the database is too large to fit into

  14. SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters.

    Science.gov (United States)

    Wang, Chunlin; Lefkowitz, Elliot J

    2004-10-28

    Large-scale sequence comparison is a powerful tool for biological inference in modern molecular biology. Comparing new sequences to those in annotated databases is a useful source of functional and structural information about these sequences. Using software such as the basic local alignment search tool (BLAST) or HMMPFAM to identify statistically significant matches between newly sequenced segments of genetic material and those in databases is an important task for most molecular biologists. Searching algorithms are intrinsically slow and data-intensive, especially in light of the rapid growth of biological sequence databases due to the emergence of high throughput DNA sequencing techniques. Thus, traditional bioinformatics tools are impractical on PCs and even on dedicated UNIX servers. To take advantage of larger databases and more reliable methods, high performance computation becomes necessary. We describe the implementation of SS-Wrapper (Similarity Search Wrapper), a package of wrapper applications that can parallelize similarity search applications on a Linux cluster. Our wrapper utilizes a query segmentation-search (QS-search) approach to parallelize sequence database search applications. It takes into consideration load balancing between each node on the cluster to maximize resource usage. QS-search is designed to wrap many different search tools, such as BLAST and HMMPFAM using the same interface. This implementation does not alter the original program, so newly obtained programs and program updates should be accommodated easily. Benchmark experiments using QS-search to optimize BLAST and HMMPFAM showed that QS-search accelerated the performance of these programs almost linearly in proportion to the number of CPUs used. We have also implemented a wrapper that utilizes a database segmentation approach (DS-BLAST) that provides a complementary solution for BLAST searches when the database is too large to fit into the memory of a single node. Used together

  15. CAZymes Analysis Toolkit (CAT): web service for searching and analyzing carbohydrate-active enzymes in a newly sequenced organism using CAZy database.

    Science.gov (United States)

    Park, Byung H; Karpinets, Tatiana V; Syed, Mustafa H; Leuze, Michael R; Uberbacher, Edward C

    2010-12-01

    The Carbohydrate-Active Enzyme (CAZy) database provides a rich set of manually annotated enzymes that degrade, modify, or create glycosidic bonds. Despite rich and invaluable information stored in the database, software tools utilizing this information for annotation of newly sequenced genomes by CAZy families are limited. We have employed two annotation approaches to fill the gap between manually curated high-quality protein sequences collected in the CAZy database and the growing number of other protein sequences produced by genome or metagenome sequencing projects. The first approach is based on a similarity search against the entire nonredundant sequences of the CAZy database. The second approach performs annotation using links or correspondences between the CAZy families and protein family domains. The links were discovered using the association rule learning algorithm applied to sequences from the CAZy database. The approaches complement each other and in combination achieved high specificity and sensitivity when cross-evaluated with the manually curated genomes of Clostridium thermocellum ATCC 27405 and Saccharophagus degradans 2-40. The capability of the proposed framework to predict the function of unknown protein domains and of hypothetical proteins in the genome of Neurospora crassa is demonstrated. The framework is implemented as a Web service, the CAZymes Analysis Toolkit, and is available at http://cricket.ornl.gov/cgi-bin/cat.cgi.

  16. BLAST and FASTA similarity searching for multiple sequence alignment.

    Science.gov (United States)

    Pearson, William R

    2014-01-01

    BLAST, FASTA, and other similarity searching programs seek to identify homologous proteins and DNA sequences based on excess sequence similarity. If two sequences share much more similarity than expected by chance, the simplest explanation for the excess similarity is common ancestry-homology. The most effective similarity searches compare protein sequences, rather than DNA sequences, for sequences that encode proteins, and use expectation values, rather than percent identity, to infer homology. The BLAST and FASTA packages of sequence comparison programs provide programs for comparing protein and DNA sequences to protein databases (the most sensitive searches). Protein and translated-DNA comparisons to protein databases routinely allow evolutionary look back times from 1 to 2 billion years; DNA:DNA searches are 5-10-fold less sensitive. BLAST and FASTA can be run on popular web sites, but can also be downloaded and installed on local computers. With local installation, target databases can be customized for the sequence data being characterized. With today's very large protein databases, search sensitivity can also be improved by searching smaller comprehensive databases, for example, a complete protein set from an evolutionarily neighboring model organism. By default, BLAST and FASTA use scoring strategies target for distant evolutionary relationships; for comparisons involving short domains or queries, or searches that seek relatively close homologs (e.g. mouse-human), shallower scoring matrices will be more effective. Both BLAST and FASTA provide very accurate statistical estimates, which can be used to reliably identify protein sequences that diverged more than 2 billion years ago.

  17. High serum folate is associated with reduced biochemical recurrence after radical prostatectomy: Results from the SEARCH Database

    Directory of Open Access Journals (Sweden)

    Daniel M. Moreira

    2013-06-01

    Full Text Available Introduction To analyze the association between serum levels of folate and risk of biochemical recurrence after radical prostatectomy among men from the Shared Equal Access Regional Cancer Hospital (SEARCH database. Materials and Methods Retrospective analysis of 135 subjects from the SEARCH database treated between 1991-2009 with available preoperative serum folate levels. Patients' characteristics at the time of the surgery were analyzed with ranksum and linear regression. Uni- and multivariable analyses of folate levels (log-transformed and time to biochemical recurrence were performed with Cox proportional hazards. Results The median preoperative folate level was 11.6ng/mL (reference = 1.5-20.0ng/mL. Folate levels were significantly lower among African-American men than Caucasians (P = 0.003. In univariable analysis, higher folate levels were associated with more recent year of surgery (P < 0.001 and lower preoperative PSA (P = 0.003. In univariable analysis, there was a trend towards lower risk of biochemical recurrence among men with high folate levels (HR = 0.61, 95%CI = 0.37-1.03, P = 0.064. After adjustments for patients characteristics' and pre- and post-operative clinical and pathological findings, higher serum levels of folate were independently associated with lower risk for biochemical recurrence (HR = 0.42, 95%CI = 0.20-0.89, P = 0.023. Conclusion In a cohort of men undergoing radical prostatectomy at several VAs across the country, higher serum folate levels were associated with lower PSA and lower risk for biochemical failure. While the source of the folate in the serum in this study is unknown (i.e. diet vs. supplement, these findings, if confirmed, suggest a potential role of folic acid supplementation or increased consumption of folate rich foods to reduce the risk of recurrence.

  18. Protocol - RPD | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...e version) File URL: ftp://ftp.biosciencedbc.jp/archive/rpd/LATEST/rpd_protocol_jp.zip File size: 535 KB Fil...e name: rpd_protocol_en.zip (English version) File URL: ftp://ftp.biosciencedbc.jp/archiv...tabase Database Description Download License Update History of This Database Site Policy | Contact Us Protocol - RPD | LSDB Archive ...

  19. On-line biomedical databases-the best source for quick search of the scientific information in the biomedicine.

    Science.gov (United States)

    Masic, Izet; Milinovic, Katarina

    2012-06-01

    Most of medical journals now has it's electronic version, available over public networks. Although there are parallel printed and electronic versions, and one other form need not to be simultaneously published. Electronic version of a journal can be published a few weeks before the printed form and must not has identical content. Electronic form of a journals may have an extension that does not contain a printed form, such as animation, 3D display, etc., or may have available fulltext, mostly in PDF or XML format, or just the contents or a summary. Access to a full text is usually not free and can be achieved only if the institution (library or host) enters into an agreement on access. Many medical journals, however, provide free access for some articles, or after a certain time (after 6 months or a year) to complete content. The search for such journals provide the network archive as High Wire Press, Free Medical Journals.com. It is necessary to allocate PubMed and PubMed Central, the first public digital archives unlimited collect journals of available medical literature, which operates in the system of the National Library of Medicine in Bethesda (USA). There are so called on- line medical journals published only in electronic form. It could be searched over on-line databases. In this paper authors shortly described about 30 data bases and short instructions how to make access and search the published papers in indexed medical journals.

  20. Tibetan Magmatism Database

    Science.gov (United States)

    Chapman, James B.; Kapp, Paul

    2017-11-01

    A database containing previously published geochronologic, geochemical, and isotopic data on Mesozoic to Quaternary igneous rocks in the Himalayan-Tibetan orogenic system are presented. The database is intended to serve as a repository for new and existing igneous rock data and is publicly accessible through a web-based platform that includes an interactive map and data table interface with search, filtering, and download options. To illustrate the utility of the database, the age, location, and ɛHft composition of magmatism from the central Gangdese batholith in the southern Lhasa terrane are compared. The data identify three high-flux events, which peak at 93, 50, and 15 Ma. They are characterized by inboard arc migration and a temporal and spatial shift to more evolved isotopic compositions.

  1. Price, performance, and the FDA approval process: the example of home HIV testing.

    Science.gov (United States)

    Paltiel, A David; Pollack, Harold A

    2010-01-01

    The Food and Drug Administration (FDA) is considering approval of an over-the-counter, rapid HIV test for home use. To support its decision, the FDA seeks evidence of the test's performance. It has asked the manufacturer to conduct field studies of the test's sensitivity and specificity when employed by untrained users. In this article, the authors argue that additional information should be sought to evaluate the prevalence of undetected HIV in the end-user The analytic framework produces the elementary but counterintuitive finding that the performance of the home HIV test- measured in terms of its ability to correctly detect the presence and absence of HIV infection among the people who purchase it-depends critically on the manufacturer's retail price. This finding has profound implications for the FDA's approval process.

  2. Regulating (for the benefit of) future persons: a different perspective on the FDA's jurisdiction to regulate human reproductive cloning.

    Science.gov (United States)

    Javitt, Gail H; Hudson, Kathy

    2003-01-01

    The Food and Drug Administration (FDA) has taken the position that human reproductive cloning falls within its regulatory jurisdiction. This position has been subject to criticism on both procedural and substantive grounds. Some have contended that the FDA has failed to follow administrative law principles in asserting its jurisdiction, while others claim the FDA is ill suited to the task of addressing the ethical and social implications of human cloning. This Article argues, that, notwithstanding these criticisms, the FDA could plausibly assert jurisdiction over human cloning as a form of human gene therapy, an area in which the FDA is already regarded as having primary regulatory authority. Such an assertion would require that the FDA's jurisdiction extend to products affecting future persons, i.e., those not yet born. This Article demonstrates, for the first time, that such jurisdiction was implicit in the enactment of the 1962 Kefauver-Harris Amendments to the Federal Food, Drug, and Cosmetic Act and that the FDA has historically relied on such authority in promulgating regulations for drugs and devices.

  3. Download - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available e Description Download License Update History of This Database Site Policy | Contact Us Download - PGDBj - Ortholog DB | LSDB Archive ... ...List Contact us PGDBj - Ortholog DB Download First of all, please read the license of this database. Data na...switchLanguage; BLAST Search Image Search Home About Archive Update History Data

  4. Predicting the performance of fingerprint similarity searching.

    Science.gov (United States)

    Vogt, Martin; Bajorath, Jürgen

    2011-01-01

    Fingerprints are bit string representations of molecular structure that typically encode structural fragments, topological features, or pharmacophore patterns. Various fingerprint designs are utilized in virtual screening and their search performance essentially depends on three parameters: the nature of the fingerprint, the active compounds serving as reference molecules, and the composition of the screening database. It is of considerable interest and practical relevance to predict the performance of fingerprint similarity searching. A quantitative assessment of the potential that a fingerprint search might successfully retrieve active compounds, if available in the screening database, would substantially help to select the type of fingerprint most suitable for a given search problem. The method presented herein utilizes concepts from information theory to relate the fingerprint feature distributions of reference compounds to screening libraries. If these feature distributions do not sufficiently differ, active database compounds that are similar to reference molecules cannot be retrieved because they disappear in the "background." By quantifying the difference in feature distribution using the Kullback-Leibler divergence and relating the divergence to compound recovery rates obtained for different benchmark classes, fingerprint search performance can be quantitatively predicted.

  5. DRUMS: a human disease related unique gene mutation search engine.

    Science.gov (United States)

    Li, Zuofeng; Liu, Xingnan; Wen, Jingran; Xu, Ye; Zhao, Xin; Li, Xuan; Liu, Lei; Zhang, Xiaoyan

    2011-10-01

    With the completion of the human genome project and the development of new methods for gene variant detection, the integration of mutation data and its phenotypic consequences has become more important than ever. Among all available resources, locus-specific databases (LSDBs) curate one or more specific genes' mutation data along with high-quality phenotypes. Although some genotype-phenotype data from LSDB have been integrated into central databases little effort has been made to integrate all these data by a search engine approach. In this work, we have developed disease related unique gene mutation search engine (DRUMS), a search engine for human disease related unique gene mutation as a convenient tool for biologists or physicians to retrieve gene variant and related phenotype information. Gene variant and phenotype information were stored in a gene-centred relational database. Moreover, the relationships between mutations and diseases were indexed by the uniform resource identifier from LSDB, or another central database. By querying DRUMS, users can access the most popular mutation databases under one interface. DRUMS could be treated as a domain specific search engine. By using web crawling, indexing, and searching technologies, it provides a competitively efficient interface for searching and retrieving mutation data and their relationships to diseases. The present system is freely accessible at http://www.scbit.org/glif/new/drums/index.html. © 2011 Wiley-Liss, Inc.

  6. Developing an Inhouse Database from Online Sources.

    Science.gov (United States)

    Smith-Cohen, Deborah

    1993-01-01

    Describes the development of an in-house bibliographic database by the U.S. Army Corp of Engineers Cold Regions Research and Engineering Laboratory on arctic wetlands research. Topics discussed include planning; identifying relevant search terms and commercial online databases; downloading citations; criteria for software selection; management…

  7. A Survey in Indexing and Searching XML Documents.

    Science.gov (United States)

    Luk, Robert W. P.; Leong, H. V.; Dillon, Tharam S.; Chan, Alvin T. S.; Croft, W. Bruce; Allan, James

    2002-01-01

    Discussion of XML focuses on indexing techniques for XML documents, grouping them into flat-file, semistructured, and structured indexing paradigms. Highlights include searching techniques, including full text search and multistage search; search result presentations; database and information retrieval system integration; XML query languages; and…

  8. Electronic biomedical literature search for budding researcher.

    Science.gov (United States)

    Thakre, Subhash B; Thakre S, Sushama S; Thakre, Amol D

    2013-09-01

    Search for specific and well defined literature related to subject of interest is the foremost step in research. When we are familiar with topic or subject then we can frame appropriate research question. Appropriate research question is the basis for study objectives and hypothesis. The Internet provides a quick access to an overabundance of the medical literature, in the form of primary, secondary and tertiary literature. It is accessible through journals, databases, dictionaries, textbooks, indexes, and e-journals, thereby allowing access to more varied, individualised, and systematic educational opportunities. Web search engine is a tool designed to search for information on the World Wide Web, which may be in the form of web pages, images, information, and other types of files. Search engines for internet-based search of medical literature include Google, Google scholar, Scirus, Yahoo search engine, etc., and databases include MEDLINE, PubMed, MEDLARS, etc. Several web-libraries (National library Medicine, Cochrane, Web of Science, Medical matrix, Emory libraries) have been developed as meta-sites, providing useful links to health resources globally. A researcher must keep in mind the strengths and limitations of a particular search engine/database while searching for a particular type of data. Knowledge about types of literature, levels of evidence, and detail about features of search engine as available, user interface, ease of access, reputable content, and period of time covered allow their optimal use and maximal utility in the field of medicine. Literature search is a dynamic and interactive process; there is no one way to conduct a search and there are many variables involved. It is suggested that a systematic search of literature that uses available electronic resource effectively, is more likely to produce quality research.

  9. A database of immunoglobulins with integrated tools: DIGIT.

    KAUST Repository

    Chailyan, Anna; Tramontano, Anna; Marcatili, Paolo

    2011-01-01

    The DIGIT (Database of ImmunoGlobulins with Integrated Tools) database (http://biocomputing.it/digit) is an integrated resource storing sequences of annotated immunoglobulin variable domains and enriched with tools for searching and analyzing them. The annotations in the database include information on the type of antigen, the respective germline sequences and on pairing information between light and heavy chains. Other annotations, such as the identification of the complementarity determining regions, assignment of their structural class and identification of mutations with respect to the germline, are computed on the fly and can also be obtained for user-submitted sequences. The system allows customized BLAST searches and automatic building of 3D models of the domains to be performed.

  10. A database of immunoglobulins with integrated tools: DIGIT.

    KAUST Repository

    Chailyan, Anna

    2011-11-10

    The DIGIT (Database of ImmunoGlobulins with Integrated Tools) database (http://biocomputing.it/digit) is an integrated resource storing sequences of annotated immunoglobulin variable domains and enriched with tools for searching and analyzing them. The annotations in the database include information on the type of antigen, the respective germline sequences and on pairing information between light and heavy chains. Other annotations, such as the identification of the complementarity determining regions, assignment of their structural class and identification of mutations with respect to the germline, are computed on the fly and can also be obtained for user-submitted sequences. The system allows customized BLAST searches and automatic building of 3D models of the domains to be performed.

  11. Intelligent methods for data retrieval in fusion databases

    International Nuclear Information System (INIS)

    Vega, J.

    2008-01-01

    The plasma behaviour is identified through the recognition of patterns inside signals. The search for patterns is usually a manual and tedious procedure in which signals need to be examined individually. A breakthrough in data retrieval for fusion databases is the development of intelligent methods to search for patterns. A pattern (in the broadest sense) could be a single segment of a waveform, a set of pixels within an image or even a heterogeneous set of features made up of waveforms, images and any kind of experimental data. Intelligent methods will allow searching for data according to technical, scientific and structural criteria instead of an identifiable time interval or pulse number. Such search algorithms should be intelligent enough to avoid passing over the entire database. Benefits of such access methods are discussed and several available techniques are reviewed. In addition, the applicability of the methods from general purpose searching systems to ad hoc developments is covered

  12. License - PSCDB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...wnload License Update History of This Database Site Policy | Contact Us License - PSCDB | LSDB Archive ...

  13. Download - RPSD | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...Download License Update History of This Database Site Policy | Contact Us Download - RPSD | LSDB Archive ...

  14. License - DMPD | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...ownload License Update History of This Database Site Policy | Contact Us License - DMPD | LSDB Archive ...

  15. Supervised learning of tools for content-based search of image databases

    Science.gov (United States)

    Delanoy, Richard L.

    1996-03-01

    A computer environment, called the Toolkit for Image Mining (TIM), is being developed with the goal of enabling users with diverse interests and varied computer skills to create search tools for content-based image retrieval and other pattern matching tasks. Search tools are generated using a simple paradigm of supervised learning that is based on the user pointing at mistakes of classification made by the current search tool. As mistakes are identified, a learning algorithm uses the identified mistakes to build up a model of the user's intentions, construct a new search tool, apply the search tool to a test image, display the match results as feedback to the user, and accept new inputs from the user. Search tools are constructed in the form of functional templates, which are generalized matched filters capable of knowledge- based image processing. The ability of this system to learn the user's intentions from experience contrasts with other existing approaches to content-based image retrieval that base searches on the characteristics of a single input example or on a predefined and semantically- constrained textual query. Currently, TIM is capable of learning spectral and textural patterns, but should be adaptable to the learning of shapes, as well. Possible applications of TIM include not only content-based image retrieval, but also quantitative image analysis, the generation of metadata for annotating images, data prioritization or data reduction in bandwidth-limited situations, and the construction of components for larger, more complex computer vision algorithms.

  16. Heuristic Search Theory and Applications

    CERN Document Server

    Edelkamp, Stefan

    2011-01-01

    Search has been vital to artificial intelligence from the very beginning as a core technique in problem solving. The authors present a thorough overview of heuristic search with a balance of discussion between theoretical analysis and efficient implementation and application to real-world problems. Current developments in search such as pattern databases and search with efficient use of external memory and parallel processing units on main boards and graphics cards are detailed. Heuristic search as a problem solving tool is demonstrated in applications for puzzle solving, game playing, constra

  17. LETTER TO THE EDITOR: Optimization of partial search

    Science.gov (United States)

    Korepin, Vladimir E.

    2005-11-01

    A quantum Grover search algorithm can find a target item in a database faster than any classical algorithm. One can trade accuracy for speed and find a part of the database (a block) containing the target item even faster; this is partial search. A partial search algorithm was recently suggested by Grover and Radhakrishnan. Here we optimize it. Efficiency of the search algorithm is measured by the number of queries to the oracle. The author suggests a new version of the Grover-Radhakrishnan algorithm which uses a minimal number of such queries. The algorithm can run on the same hardware that is used for the usual Grover algorithm.

  18. 21 CFR 5.1110 - FDA public information offices.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 1 2010-04-01 2010-04-01 false FDA public information offices. 5.1110 Section 5.1110 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL...) Press Relations Staff. Press offices are located in White Oak Bldg. 1, 10903 New Hampshire Ave., Silver...

  19. Database of Legal Terms for Communicative and Knowledge Information Tools

    DEFF Research Database (Denmark)

    Nielsen, Sandro

    2014-01-01

    foundations of online dictionaries in light of the technical options available for online information tools combined with modern lexicographic principles. The above discussion indicates that the legal database is a repository of structured data serving online dictionaries that search for data in databases......, retrieve the relevant data, and present them to users in predetermined ways. Lawyers, students and translators can thus access the data through targeted searches relating directly to the problems they need to solve, because search engines are designed according to dictionary functions, i.e. the type...

  20. The impact of electronic cigarettes on the paediatric population

    OpenAIRE

    Durmowicz, Elizabeth L

    2014-01-01

    Objective To review the impact of electronic cigarettes (e-cigarettes) on children. Methods Five electronic databases were searched through 31 December 2013. Studies in English that included data for children younger than 18 years of age were included. In addition, relevant data from articles identified during searches of the e-cigarette literature, relevant state survey data and paediatric voluntary adverse event reports submitted to the US Food and Drug Administration (FDA) were reviewed an...

  1. Download - SSBD | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...ion Download License Update History of This Database Site Policy | Contact Us Download - SSBD | LSDB Archive ...

  2. Point-Counterpoint: The FDA Has a Role in Regulation of Laboratory-Developed Tests.

    Science.gov (United States)

    Caliendo, Angela M; Hanson, Kimberly E

    2016-04-01

    Since the Food and Drug Administration (FDA) released its draft guidance on the regulation of laboratory-developed tests (LDTs) in October 2014, there has been a flurry of responses from commercial and hospital-based laboratory directors, clinicians, professional organizations, and diagnostic companies. The FDA defines an LDT as an "in vitrodiagnostic device that is intended for clinical use and is designed, manufactured, and used within a single laboratory." The draft guidance outlines a risk-based approach, with oversight of high-risk and moderate-risk tests being phased in over 9 years. High-risk tests would be regulated first and require premarket approval. Subsequently, moderate-risk tests would require a 510(k) premarket submission to the FDA and low-risk tests would need only to be registered. Oversight discretion would be exercised for LDTs focused on rare diseases (defined as fewer than 4,000 tests, not cases, per year nationally) and unmet clinical needs (defined as those tests for which there is no alternative FDA-cleared or -approved test). There was an open comment period followed by a public hearing in early January of 2015, and we are currently awaiting the final decision regarding the regulation of LDTs. Given that LDTs have been developed by many laboratories and are essential for the diagnosis and monitoring of an array of infectious diseases, changes in their regulation will have far-reaching implications for clinical microbiology laboratories. In this Point-Counterpoint, Angela Caliendo discusses the potential benefits of the FDA guidance for LDTs whereas Kim Hanson discusses the concerns associated with implementing the guidance and why these regulations may not improve clinical care. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  3. Design and implementation of the NPOI database and website

    Science.gov (United States)

    Newman, K.; Jorgensen, A. M.; Landavazo, M.; Sun, B.; Hutter, D. J.; Armstrong, J. T.; Mozurkewich, David; Elias, N.; van Belle, G. T.; Schmitt, H. R.; Baines, E. K.

    2014-07-01

    The Navy Precision Optical Interferometer (NPOI) has been recording astronomical observations for nearly two decades, at this point with hundreds of thousands of individual observations recorded to date for a total data volume of many terabytes. To make maximum use of the NPOI data it is necessary to organize them in an easily searchable manner and be able to extract essential diagnostic information from the data to allow users to quickly gauge data quality and suitability for a specific science investigation. This sets the motivation for creating a comprehensive database of observation metadata as well as, at least, reduced data products. The NPOI database is implemented in MySQL using standard database tools and interfaces. The use of standard database tools allows us to focus on top-level database and interface implementation and take advantage of standard features such as backup, remote access, mirroring, and complex queries which would otherwise be time-consuming to implement. A website was created in order to give scientists a user friendly interface for searching the database. It allows the user to select various metadata to search for and also allows them to decide how and what results are displayed. This streamlines the searches, making it easier and quicker for scientists to find the information they are looking for. The website has multiple browser and device support. In this paper we present the design of the NPOI database and website, and give examples of its use.

  4. Gaps, tensions, and conflicts in the FDA approval process: implications for clinical practice.

    Science.gov (United States)

    Deyo, Richard A

    2004-01-01

    Despite many successes, drug approval at the Food and Drug Administration (FDA) is subject to gaps, internal tensions, and conflicts of interest. Recalls of drugs and devices and studies demonstrating advantages of older drugs over newer ones highlight the importance of these limitations. The FDA does not compare competing drugs and rarely requires tests of clinical efficacy for new devices. It does not review advertisements before use, assess cost-effectiveness, or regulate surgery (except for devices). Many believe postmarketing surveillance of drugs and devices is inadequate. A source of tension within the agency is pressure for speedy approvals. This may have resulted in "burn-out" among medical officers and has prompted criticism that safety is ignored. Others argue, however, that the agency is unnecessarily slow and bureaucratic. Recent reports identify conflicts of interest (stock ownership, consulting fees, research grants) among some members of the FDA's advisory committees. FDA review serves a critical function, but physicians should be aware that new drugs may not be as effective as old ones; that new drugs are likely to have undiscovered side effects at the time of marketing; that direct-to-consumer ads are sometimes misleading; that new devices generally have less rigorous evidence of efficacy than new drugs; and that value for money is not considered in approval.

  5. Policy implications for familial searching.

    Science.gov (United States)

    Kim, Joyce; Mammo, Danny; Siegel, Marni B; Katsanis, Sara H

    2011-11-01

    In the United States, several states have made policy decisions regarding whether and how to use familial searching of the Combined DNA Index System (CODIS) database in criminal investigations. Familial searching pushes DNA typing beyond merely identifying individuals to detecting genetic relatedness, an application previously reserved for missing persons identifications and custody battles. The intentional search of CODIS for partial matches to an item of evidence offers law enforcement agencies a powerful tool for developing investigative leads, apprehending criminals, revitalizing cold cases and exonerating wrongfully convicted individuals. As familial searching involves a range of logistical, social, ethical and legal considerations, states are now grappling with policy options for implementing familial searching to balance crime fighting with its potential impact on society. When developing policies for familial searching, legislators should take into account the impact of familial searching on select populations and the need to minimize personal intrusion on relatives of individuals in the DNA database. This review describes the approaches used to narrow a suspect pool from a partial match search of CODIS and summarizes the economic, ethical, logistical and political challenges of implementing familial searching. We examine particular US state policies and the policy options adopted to address these issues. The aim of this review is to provide objective background information on the controversial approach of familial searching to inform policy decisions in this area. Herein we highlight key policy options and recommendations regarding effective utilization of familial searching that minimize harm to and afford maximum protection of US citizens.

  6. Citation searching: a systematic review case study of multiple risk behaviour interventions.

    Science.gov (United States)

    Wright, Kath; Golder, Su; Rodriguez-Lopez, Rocio

    2014-06-03

    The value of citation searches as part of the systematic review process is currently unknown. While the major guides to conducting systematic reviews state that citation searching should be carried out in addition to searching bibliographic databases there are still few studies in the literature that support this view. Rather than using a predefined search strategy to retrieve studies, citation searching uses known relevant papers to identify further papers. We describe a case study about the effectiveness of using the citation sources Google Scholar, Scopus, Web of Science and OVIDSP MEDLINE to identify records for inclusion in a systematic review.We used the 40 included studies identified by traditional database searches from one systematic review of interventions for multiple risk behaviours. We searched for each of the included studies in the four citation sources to retrieve the details of all papers that have cited these studies.We carried out two analyses; the first was to examine the overlap between the four citation sources to identify which citation tool was the most useful; the second was to investigate whether the citation searches identified any relevant records in addition to those retrieved by the original database searches. The highest number of citations was retrieved from Google Scholar (1680), followed by Scopus (1173), then Web of Science (1095) and lastly OVIDSP (213). To retrieve all the records identified by the citation tracking searching all four resources was required. Google Scholar identified the highest number of unique citations.The citation tracking identified 9 studies that met the review's inclusion criteria. Eight of these had already been identified by the traditional databases searches and identified in the screening process while the ninth was not available in any of the databases when the original searches were carried out. It would, however, have been identified by two of the database search strategies if searches had been

  7. The Lung Image Database Consortium (LIDC) and Image Database Resource Initiative (IDRI): A Completed Reference Database of Lung Nodules on CT Scans

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2011-02-15

    Purpose: The development of computer-aided diagnostic (CAD) methods for lung nodule detection, classification, and quantitative assessment can be facilitated through a well-characterized repository of computed tomography (CT) scans. The Lung Image Database Consortium (LIDC) and Image Database Resource Initiative (IDRI) completed such a database, establishing a publicly available reference for the medical imaging research community. Initiated by the National Cancer Institute (NCI), further advanced by the Foundation for the National Institutes of Health (FNIH), and accompanied by the Food and Drug Administration (FDA) through active participation, this public-private partnership demonstrates the success of a consortium founded on a consensus-based process. Methods: Seven academic centers and eight medical imaging companies collaborated to identify, address, and resolve challenging organizational, technical, and clinical issues to provide a solid foundation for a robust database. The LIDC/IDRI Database contains 1018 cases, each of which includes images from a clinical thoracic CT scan and an associated XML file that records the results of a two-phase image annotation process performed by four experienced thoracic radiologists. In the initial blinded-read phase, each radiologist independently reviewed each CT scan and marked lesions belonging to one of three categories (''nodule{>=}3 mm,''''nodule<3 mm,'' and ''non-nodule{>=}3 mm''). In the subsequent unblinded-read phase, each radiologist independently reviewed their own marks along with the anonymized marks of the three other radiologists to render a final opinion. The goal of this process was to identify as completely as possible all lung nodules in each CT scan without requiring forced consensus. Results: The Database contains 7371 lesions marked ''nodule'' by at least one radiologist. 2669 of these lesions were marked &apos

  8. View discovery in OLAP databases through statistical combinatorial optimization

    Energy Technology Data Exchange (ETDEWEB)

    Hengartner, Nick W [Los Alamos National Laboratory; Burke, John [PNNL; Critchlow, Terence [PNNL; Joslyn, Cliff [PNNL; Hogan, Emilie [PNNL

    2009-01-01

    OnLine Analytical Processing (OLAP) is a relational database technology providing users with rapid access to summary, aggregated views of a single large database, and is widely recognized for knowledge representation and discovery in high-dimensional relational databases. OLAP technologies provide intuitive and graphical access to the massively complex set of possible summary views available in large relational (SQL) structured data repositories. The capability of OLAP database software systems to handle data complexity comes at a high price for analysts, presenting them a combinatorially vast space of views of a relational database. We respond to the need to deploy technologies sufficient to allow users to guide themselves to areas of local structure by casting the space of 'views' of an OLAP database as a combinatorial object of all projections and subsets, and 'view discovery' as an search process over that lattice. We equip the view lattice with statistical information theoretical measures sufficient to support a combinatorial optimization process. We outline 'hop-chaining' as a particular view discovery algorithm over this object, wherein users are guided across a permutation of the dimensions by searching for successive two-dimensional views, pushing seen dimensions into an increasingly large background filter in a 'spiraling' search process. We illustrate this work in the context of data cubes recording summary statistics for radiation portal monitors at US ports.

  9. Download - DGBY | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...base Description Download License Update History of This Database Site Policy | Contact Us Download - DGBY | LSDB Archive ...

  10. The comparative recall of Google Scholar versus PubMed in identical searches for biomedical systematic reviews: a review of searches used in systematic reviews.

    Science.gov (United States)

    Bramer, Wichor M; Giustini, Dean; Kramer, Bianca Mr; Anderson, Pf

    2013-12-23

    The usefulness of Google Scholar (GS) as a bibliographic database for biomedical systematic review (SR) searching is a subject of current interest and debate in research circles. Recent research has suggested GS might even be used alone in SR searching. This assertion is challenged here by testing whether GS can locate all studies included in 21 previously published SRs. Second, it examines the recall of GS, taking into account the maximum number of items that can be viewed, and tests whether more complete searches created by an information specialist will improve recall compared to the searches used in the 21 published SRs. The authors identified 21 biomedical SRs that had used GS and PubMed as information sources and reported their use of identical, reproducible search strategies in both databases. These search strategies were rerun in GS and PubMed, and analyzed as to their coverage and recall. Efforts were made to improve searches that underperformed in each database. GS' overall coverage was higher than PubMed (98% versus 91%) and overall recall is higher in GS: 80% of the references included in the 21 SRs were returned by the original searches in GS versus 68% in PubMed. Only 72% of the included references could be used as they were listed among the first 1,000 hits (the maximum number shown). Practical precision (the number of included references retrieved in the first 1,000, divided by 1,000) was on average 1.9%, which is only slightly lower than in other published SRs. Improving searches with the lowest recall resulted in an increase in recall from 48% to 66% in GS and, in PubMed, from 60% to 85%. Although its coverage and precision are acceptable, GS, because of its incomplete recall, should not be used as a single source in SR searching. A specialized, curated medical database such as PubMed provides experienced searchers with tools and functionality that help improve recall, and numerous options in order to optimize precision. Searches for SRs should be

  11. Software-Related Recalls of Health Information Technology and Other Medical Devices: Implications for FDA Regulation of Digital Health.

    Science.gov (United States)

    Ronquillo, Jay G; Zuckerman, Diana M

    2017-09-01

    Policy Points: Medical software has become an increasingly critical component of health care, yet the regulation of these devices is inconsistent and controversial. No studies of medical devices and software assess the impact on patient safety of the FDA's current regulatory safeguards and new legislative changes to those standards. Our analysis quantifies the impact of software problems in regulated medical devices and indicates that current regulations are necessary but not sufficient for ensuring patient safety by identifying and eliminating dangerous defects in software currently on the market. New legislative changes will further deregulate health IT, reducing safeguards that facilitate the reporting and timely recall of flawed medical software that could harm patients. Medical software has become an increasingly critical component of health care, yet the regulatory landscape for digital health is inconsistent and controversial. To understand which policies might best protect patients, we examined the impact of the US Food and Drug Administration's (FDA's) regulatory safeguards on software-related technologies in recent years and the implications for newly passed legislative changes in regulatory policy. Using FDA databases, we identified all medical devices that were recalled from 2011 through 2015 primarily because of software defects. We counted all software-related recalls for each FDA risk category and evaluated each high-risk and moderate-risk recall of electronic medical records to determine the manufacturer, device classification, submission type, number of units, and product details. A total of 627 software devices (1.4 million units) were subject to recalls, with 12 of these devices (190,596 units) subject to the highest-risk recalls. Eleven of the devices recalled as high risk had entered the market through the FDA review process that does not require evidence of safety or effectiveness, and one device was completely exempt from regulatory review

  12. NESSY, a relational PC database for nuclear structure and decay data

    International Nuclear Information System (INIS)

    Boboshin, I.N.; Varlamov, V.V.; Trukhanov, S.K.

    1994-11-01

    The universal relational database NESSY (New ENSDF Search SYstem) based on the international ENSDF system (Evaluated Nuclear Structure Data File) is described. NESSY, which was developed for IBM compatible PC, provides high efficiency processing of ENSDF information for searches and retrievals of nuclear physics data. The principle of the database development and examples of applications are presented. (author)

  13. OrChem - An open source chemistry search engine for Oracle®

    Science.gov (United States)

    2009-01-01

    Background Registration, indexing and searching of chemical structures in relational databases is one of the core areas of cheminformatics. However, little detail has been published on the inner workings of search engines and their development has been mostly closed-source. We decided to develop an open source chemistry extension for Oracle, the de facto database platform in the commercial world. Results Here we present OrChem, an extension for the Oracle 11G database that adds registration and indexing of chemical structures to support fast substructure and similarity searching. The cheminformatics functionality is provided by the Chemistry Development Kit. OrChem provides similarity searching with response times in the order of seconds for databases with millions of compounds, depending on a given similarity cut-off. For substructure searching, it can make use of multiple processor cores on today's powerful database servers to provide fast response times in equally large data sets. Availability OrChem is free software and can be redistributed and/or modified under the terms of the GNU Lesser General Public License as published by the Free Software Foundation. All software is available via http://orchem.sourceforge.net. PMID:20298521

  14. OrChem - An open source chemistry search engine for Oracle(R).

    Science.gov (United States)

    Rijnbeek, Mark; Steinbeck, Christoph

    2009-10-22

    Registration, indexing and searching of chemical structures in relational databases is one of the core areas of cheminformatics. However, little detail has been published on the inner workings of search engines and their development has been mostly closed-source. We decided to develop an open source chemistry extension for Oracle, the de facto database platform in the commercial world. Here we present OrChem, an extension for the Oracle 11G database that adds registration and indexing of chemical structures to support fast substructure and similarity searching. The cheminformatics functionality is provided by the Chemistry Development Kit. OrChem provides similarity searching with response times in the order of seconds for databases with millions of compounds, depending on a given similarity cut-off. For substructure searching, it can make use of multiple processor cores on today's powerful database servers to provide fast response times in equally large data sets. OrChem is free software and can be redistributed and/or modified under the terms of the GNU Lesser General Public License as published by the Free Software Foundation. All software is available via http://orchem.sourceforge.net.

  15. Medical student appraisal: searching on smartphones.

    Science.gov (United States)

    Khalifian, S; Markman, T; Sampognaro, P; Mitchell, S; Weeks, S; Dattilo, J

    2013-01-01

    The rapidly growing industry for mobile medical applications provides numerous smartphone resources designed for healthcare professionals. However, not all applications are equally useful in addressing the questions of early medical trainees. Three popular, free, mobile healthcare applications were evaluated along with a Google(TM) web search on both Apple(TM) and Android(TM) devices. Six medical students at a large academic hospital evaluated each application for a one-week period while on various clinical rotations. Google(TM) was the most frequently used search method and presented multimedia resources but was inefficient for obtaining clinical management information. Epocrates(TM) Pill ID feature was praised for its clinical utility. Medscape(TM) had the highest satisfaction of search and excelled through interactive educational features. Micromedex(TM) offered both FDA and off-label dosing for drugs. Google(TM) was the preferred search method for questions related to basic disease processes and multimedia resources, but was inadequate for clinical management. Caution should also be exercised when using Google(TM) in front of patients. Medscape(TM) was the most appealing application due to a broad scope of content and educational features relevant to medical trainees. Students should also be cognizant of how mobile technology may be perceived by their evaluators to avoid false impressions.

  16. Computer system for International Reactor Pressure Vessel Materials Database support

    International Nuclear Information System (INIS)

    Arutyunjan, R.; Kabalevsky, S.; Kiselev, V.; Serov, A.

    1997-01-01

    This report presents description of the computer tools for support of International Reactor Pressure Vessel Materials Database developed at IAEA. Work was focused on raw, qualified, processed materials data, search, retrieval, analysis, presentation and export possibilities of data. Developed software has the following main functions: provides software tools for querying and search of any type of data in the database; provides the capability to update the existing information in the database; provides the capability to present and print selected data; provides the possibility of export on yearly basis the run-time IRPVMDB with raw, qualified and processed materials data to Database members; provides the capability to export any selected sets of raw, qualified, processed materials data

  17. LSE-Sign: A lexical database for Spanish Sign Language.

    Science.gov (United States)

    Gutierrez-Sigut, Eva; Costello, Brendan; Baus, Cristina; Carreiras, Manuel

    2016-03-01

    The LSE-Sign database is a free online tool for selecting Spanish Sign Language stimulus materials to be used in experiments. It contains 2,400 individual signs taken from a recent standardized LSE dictionary, and a further 2,700 related nonsigns. Each entry is coded for a wide range of grammatical, phonological, and articulatory information, including handshape, location, movement, and non-manual elements. The database is accessible via a graphically based search facility which is highly flexible both in terms of the search options available and the way the results are displayed. LSE-Sign is available at the following website: http://www.bcbl.eu/databases/lse/.

  18. We really need to talk: adapting FDA processes to rapid change.

    Science.gov (United States)

    Lykken, Sara

    2013-01-01

    The rapidly evolving realm of modern commerce strains traditional regulatory paradigms. This paper traces the historical evolution of FDA crisis-response regulation and provides examples of ways in which the definitions and procedures resulting from that past continue to be challenged by new products as market entrants, some in good faith and others not, take actions that create disconnects between actual product and marketing controls and those that consumers might expect. The paper then explores some of the techniques used by other federal agencies that have faced similar challenges in environments characterized by rapid innovation, and draws from this analysis suggestions for improvement of the FDA's warning letter system.

  19. Policy implications for familial searching

    OpenAIRE

    Kim, Joyce; Mammo, Danny; Siegel, Marni B; Katsanis, Sara H

    2011-01-01

    Abstract In the United States, several states have made policy decisions regarding whether and how to use familial searching of the Combined DNA Index System (CODIS) database in criminal investigations. Familial searching pushes DNA typing beyond merely identifying individuals to detecting genetic relatedness, an application previously reserved for missing persons identifications and custody battles. The intentional search of CODIS for partial matches to an item of evidence offers law enforce...

  20. Comparing the Precision of Information Retrieval of MeSH-Controlled Vocabulary Search Method and a Visual Method in the Medline Medical Database.

    Science.gov (United States)

    Hariri, Nadjla; Ravandi, Somayyeh Nadi

    2014-01-01

    Medline is one of the most important databases in the biomedical field. One of the most important hosts for Medline is Elton B. Stephens CO. (EBSCO), which has presented different search methods that can be used based on the needs of the users. Visual search and MeSH-controlled search methods are among the most common methods. The goal of this research was to compare the precision of the retrieved sources in the EBSCO Medline base using MeSH-controlled and visual search methods. This research was a semi-empirical study. By holding training workshops, 70 students of higher education in different educational departments of Kashan University of Medical Sciences were taught MeSH-Controlled and visual search methods in 2012. Then, the precision of 300 searches made by these students was calculated based on Best Precision, Useful Precision, and Objective Precision formulas and analyzed in SPSS software using the independent sample T Test, and three precisions obtained with the three precision formulas were studied for the two search methods. The mean precision of the visual method was greater than that of the MeSH-Controlled search for all three types of precision, i.e. Best Precision, Useful Precision, and Objective Precision, and their mean precisions were significantly different (P searches. Fifty-three percent of the participants in the research also mentioned that the use of the combination of the two methods produced better results. For users, it is more appropriate to use a natural, language-based method, such as the visual method, in the EBSCO Medline host than to use the controlled method, which requires users to use special keywords. The potential reason for their preference was that the visual method allowed them more freedom of action.

  1. The MAJORANA Parts Tracking Database

    Science.gov (United States)

    Abgrall, N.; Aguayo, E.; Avignone, F. T.; Barabash, A. S.; Bertrand, F. E.; Brudanin, V.; Busch, M.; Byram, D.; Caldwell, A. S.; Chan, Y.-D.; Christofferson, C. D.; Combs, D. C.; Cuesta, C.; Detwiler, J. A.; Doe, P. J.; Efremenko, Yu.; Egorov, V.; Ejiri, H.; Elliott, S. R.; Esterline, J.; Fast, J. E.; Finnerty, P.; Fraenkle, F. M.; Galindo-Uribarri, A.; Giovanetti, G. K.; Goett, J.; Green, M. P.; Gruszko, J.; Guiseppe, V. E.; Gusev, K.; Hallin, A. L.; Hazama, R.; Hegai, A.; Henning, R.; Hoppe, E. W.; Howard, S.; Howe, M. A.; Keeter, K. J.; Kidd, M. F.; Kochetov, O.; Konovalov, S. I.; Kouzes, R. T.; LaFerriere, B. D.; Leon, J. Diaz; Leviner, L. E.; Loach, J. C.; MacMullin, J.; Martin, R. D.; Meijer, S. J.; Mertens, S.; Miller, M. L.; Mizouni, L.; Nomachi, M.; Orrell, J. L.; O`Shaughnessy, C.; Overman, N. R.; Petersburg, R.; Phillips, D. G.; Poon, A. W. P.; Pushkin, K.; Radford, D. C.; Rager, J.; Rielage, K.; Robertson, R. G. H.; Romero-Romero, E.; Ronquest, M. C.; Shanks, B.; Shima, T.; Shirchenko, M.; Snavely, K. J.; Snyder, N.; Soin, A.; Suriano, A. M.; Tedeschi, D.; Thompson, J.; Timkin, V.; Tornow, W.; Trimble, J. E.; Varner, R. L.; Vasilyev, S.; Vetter, K.; Vorren, K.; White, B. R.; Wilkerson, J. F.; Wiseman, C.; Xu, W.; Yakushev, E.; Young, A. R.; Yu, C.-H.; Yumatov, V.; Zhitnikov, I.

    2015-04-01

    The MAJORANA DEMONSTRATOR is an ultra-low background physics experiment searching for the neutrinoless double beta decay of 76Ge. The MAJORANA Parts Tracking Database is used to record the history of components used in the construction of the DEMONSTRATOR. The tracking implementation takes a novel approach based on the schema-free database technology CouchDB. Transportation, storage, and processes undergone by parts such as machining or cleaning are linked to part records. Tracking parts provide a great logistics benefit and an important quality assurance reference during construction. In addition, the location history of parts provides an estimate of their exposure to cosmic radiation. A web application for data entry and a radiation exposure calculator have been developed as tools for achieving the extreme radio-purity required for this rare decay search.

  2. The MAJORANA Parts Tracking Database

    Energy Technology Data Exchange (ETDEWEB)

    Abgrall, N. [Nuclear Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA (United States); Aguayo, E. [Pacific Northwest National Laboratory, Richland, WA (United States); Avignone, F.T. [Department of Physics and Astronomy, University of South Carolina, Columbia, SC (United States); Oak Ridge National Laboratory, Oak Ridge, TN (United States); Barabash, A.S. [Institute for Theoretical and Experimental Physics, Moscow (Russian Federation); Bertrand, F.E. [Oak Ridge National Laboratory, Oak Ridge, TN (United States); Brudanin, V. [Joint Institute for Nuclear Research, Dubna (Russian Federation); Busch, M. [Department of Physics, Duke University, Durham, NC (United States); Triangle Universities Nuclear Laboratory, Durham, NC (United States); Byram, D. [Department of Physics, University of South Dakota, Vermillion, SD (United States); Caldwell, A.S. [South Dakota School of Mines and Technology, Rapid City, SD (United States); Chan, Y-D. [Nuclear Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA (United States); Christofferson, C.D. [South Dakota School of Mines and Technology, Rapid City, SD (United States); Combs, D.C. [Department of Physics, North Carolina State University, Raleigh, NC (United States); Triangle Universities Nuclear Laboratory, Durham, NC (United States); Cuesta, C.; Detwiler, J.A.; Doe, P.J. [Center for Experimental Nuclear Physics and Astrophysics, and Department of Physics, University of Washington, Seattle, WA (United States); Efremenko, Yu. [Department of Physics and Astronomy, University of Tennessee, Knoxville, TN (United States); Egorov, V. [Joint Institute for Nuclear Research, Dubna (Russian Federation); Ejiri, H. [Research Center for Nuclear Physics and Department of Physics, Osaka University, Ibaraki, Osaka (Japan); Elliott, S.R. [Los Alamos National Laboratory, Los Alamos, NM (United States); and others

    2015-04-11

    The MAJORANA DEMONSTRATOR is an ultra-low background physics experiment searching for the neutrinoless double beta decay of {sup 76}Ge. The MAJORANA Parts Tracking Database is used to record the history of components used in the construction of the DEMONSTRATOR. The tracking implementation takes a novel approach based on the schema-free database technology CouchDB. Transportation, storage, and processes undergone by parts such as machining or cleaning are linked to part records. Tracking parts provide a great logistics benefit and an important quality assurance reference during construction. In addition, the location history of parts provides an estimate of their exposure to cosmic radiation. A web application for data entry and a radiation exposure calculator have been developed as tools for achieving the extreme radio-purity required for this rare decay search.

  3. RaftProt: mammalian lipid raft proteome database.

    Science.gov (United States)

    Shah, Anup; Chen, David; Boda, Akash R; Foster, Leonard J; Davis, Melissa J; Hill, Michelle M

    2015-01-01

    RaftProt (http://lipid-raft-database.di.uq.edu.au/) is a database of mammalian lipid raft-associated proteins as reported in high-throughput mass spectrometry studies. Lipid rafts are specialized membrane microdomains enriched in cholesterol and sphingolipids thought to act as dynamic signalling and sorting platforms. Given their fundamental roles in cellular regulation, there is a plethora of information on the size, composition and regulation of these membrane microdomains, including a large number of proteomics studies. To facilitate the mining and analysis of published lipid raft proteomics studies, we have developed a searchable database RaftProt. In addition to browsing the studies, performing basic queries by protein and gene names, searching experiments by cell, tissue and organisms; we have implemented several advanced features to facilitate data mining. To address the issue of potential bias due to biochemical preparation procedures used, we have captured the lipid raft preparation methods and implemented advanced search option for methodology and sample treatment conditions, such as cholesterol depletion. Furthermore, we have identified a list of high confidence proteins, and enabled searching only from this list of likely bona fide lipid raft proteins. Given the apparent biological importance of lipid raft and their associated proteins, this database would constitute a key resource for the scientific community. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  4. Pre-Service Teachers' Use of Library Databases: Some Insights

    Science.gov (United States)

    Lamb, Janeen; Howard, Sarah; Easey, Michael

    2014-01-01

    The aim of this study is to investigate if providing mathematics education pre-service teachers with animated library tutorials on library and database searches changes their searching practices. This study involved the completion of a survey by 138 students and seven individual interviews before and after library search demonstration videos were…

  5. Development of a biomarkers database for the National Children's Study

    Energy Technology Data Exchange (ETDEWEB)

    Lobdell, Danelle T [US Environmental Protection Agency, Office of Research and Development, National Health and Environmental Effects Research Laboratory, Human Studies Division, Epidemiology and Biomarkers Branch, MD 58A, Research Triangle Park, NC 27711 (United States); Mendola, Pauline [US Environmental Protection Agency, Office of Research and Development, National Health and Environmental Effects Research Laboratory, Human Studies Division, Epidemiology and Biomarkers Branch, MD 58A, Research Triangle Park, NC 27711 (United States)

    2005-08-07

    The National Children's Study (NCS) is a federally-sponsored, longitudinal study of environmental influences on the health and development of children across the United States (www.nationalchildrensstudy.gov). Current plans are to study approximately 100,000 children and their families beginning before birth up to age 21 years. To explore potential biomarkers that could be important measurements in the NCS, we compiled the relevant scientific literature to identify both routine or standardized biological markers as well as new and emerging biological markers. Although the search criteria encouraged examination of factors that influence the breadth of child health and development, attention was primarily focused on exposure, susceptibility, and outcome biomarkers associated with four important child health outcomes: autism and neurobehavioral disorders, injury, cancer, and asthma. The Biomarkers Database was designed to allow users to: (1) search the biomarker records compiled by type of marker (susceptibility, exposure or effect), sampling media (e.g., blood, urine, etc.), and specific marker name; (2) search the citations file; and (3) read the abstract evaluations relative to our search criteria. A searchable, user-friendly database of over 2000 articles was created and is publicly available at: http://cfpub.epa.gov/ncea/cfm/recordisplay.cfm?deid=85844. PubMed was the primary source of references with some additional searches of Toxline, NTIS, and other reference databases. Our initial focus was on review articles, beginning as early as 1996, supplemented with searches of the recent primary research literature from 2001 to 2003. We anticipate this database will have applicability for the NCS as well as other studies of children's environmental health.

  6. Development of a biomarkers database for the National Children's Study

    International Nuclear Information System (INIS)

    Lobdell, Danelle T.; Mendola, Pauline

    2005-01-01

    The National Children's Study (NCS) is a federally-sponsored, longitudinal study of environmental influences on the health and development of children across the United States (www.nationalchildrensstudy.gov). Current plans are to study approximately 100,000 children and their families beginning before birth up to age 21 years. To explore potential biomarkers that could be important measurements in the NCS, we compiled the relevant scientific literature to identify both routine or standardized biological markers as well as new and emerging biological markers. Although the search criteria encouraged examination of factors that influence the breadth of child health and development, attention was primarily focused on exposure, susceptibility, and outcome biomarkers associated with four important child health outcomes: autism and neurobehavioral disorders, injury, cancer, and asthma. The Biomarkers Database was designed to allow users to: (1) search the biomarker records compiled by type of marker (susceptibility, exposure or effect), sampling media (e.g., blood, urine, etc.), and specific marker name; (2) search the citations file; and (3) read the abstract evaluations relative to our search criteria. A searchable, user-friendly database of over 2000 articles was created and is publicly available at: http://cfpub.epa.gov/ncea/cfm/recordisplay.cfm?deid=85844. PubMed was the primary source of references with some additional searches of Toxline, NTIS, and other reference databases. Our initial focus was on review articles, beginning as early as 1996, supplemented with searches of the recent primary research literature from 2001 to 2003. We anticipate this database will have applicability for the NCS as well as other studies of children's environmental health

  7. Pharmacophore definition and 3D searches.

    Science.gov (United States)

    Langer, T; Wolber, G

    2004-12-01

    The most common pharmacophore building concepts based on either 3D structure of the target or ligand information are discussed together with the application of such models as queries for 3D database search. An overview of the key techniques available on the market is given and differences with respect to algorithms used and performance obtained are highlighted. Pharmacophore modelling and 3D database search are shown to be successful tools for enriching screening experiments aimed at the discovery of novel bio-active compounds.: © 2004 Elsevier Ltd . All rights reserved.

  8. Kazusa Marker DataBase: a database for genomics, genetics, and molecular breeding in plants

    Science.gov (United States)

    Shirasawa, Kenta; Isobe, Sachiko; Tabata, Satoshi; Hirakawa, Hideki

    2014-01-01

    In order to provide useful genomic information for agronomical plants, we have established a database, the Kazusa Marker DataBase (http://marker.kazusa.or.jp). This database includes information on DNA markers, e.g., SSR and SNP markers, genetic linkage maps, and physical maps, that were developed at the Kazusa DNA Research Institute. Keyword searches for the markers, sequence data used for marker development, and experimental conditions are also available through this database. Currently, 10 plant species have been targeted: tomato (Solanum lycopersicum), pepper (Capsicum annuum), strawberry (Fragaria × ananassa), radish (Raphanus sativus), Lotus japonicus, soybean (Glycine max), peanut (Arachis hypogaea), red clover (Trifolium pratense), white clover (Trifolium repens), and eucalyptus (Eucalyptus camaldulensis). In addition, the number of plant species registered in this database will be increased as our research progresses. The Kazusa Marker DataBase will be a useful tool for both basic and applied sciences, such as genomics, genetics, and molecular breeding in crops. PMID:25320561

  9. Search across Different Media: Numeric Data Sets and Text Files

    Directory of Open Access Journals (Sweden)

    Michael Buckland

    2006-12-01

    Full Text Available Digital technology encourages the hope of searching across and between different media forms (text, sound, image, numeric data. Topic searches are described in two different media: text files and socioeconomic numeric databases and also for transverse searching, whereby retrieved text is used to find topically related numeric data and vice versa. Direct transverse searching across different media is impossible. Descriptive metadata provide enabling infrastructure, but usually require mappings between different vocabularies and a search-term recommender system. Statistical association techniques and natural-language processing can help. Searches in socioeconomic numeric databases ordinarily require that place and time be specified.

  10. Online Searching at 9600 Baud.

    Science.gov (United States)

    Scott, Ralph Lee; Scott, Nancy Sue Schell

    1991-01-01

    Discusses online searching with the new 9600 baud rate and describes test searches on the BRS, Data-Star, LEXIS, and Dow Jones databases through three packet-switching networks: US Sprint, MEADNET, and TYMNET. Hardware and software are described, data communications equipment standards are discussed, and the impact of higher baud rates on pricing…

  11. Usefulness of [18F]-DA and [18F]-DOPA for PET imaging in a mouse model of pheochromocytoma

    International Nuclear Information System (INIS)

    Martiniova, Lucia; Cleary, Susannah; Lai, Edwin W.; Kiesewetter, Dale O.; Seidel, Jurgen; Dawson, Linda F.; Phillips, Jacqueline K.; Thomasson, David; Chen Xiaoyuan; Eisenhofer, Graeme; Powers, James F.; Kvetnansky, Richard

    2012-01-01

    Purpose: To evaluate the usefulness of [ 18 F]-6-fluorodopamine ([ 18 F]-DA) and [ 18 F]-L-6-fluoro-3,4-dihydroxyphenylalanine ([ 18 F]-DOPA) positron emission tomography (PET) in the detection of subcutaneous (s.c.) and metastatic pheochromocytoma in mice; to assess the expression of the norepinephrine transporter (NET) and vesicular monoamine transporters 1 and 2 (VMAT1 and VMAT2), all important for [ 18 F]-DA and [ 18 F]-DOPA uptake. Furthermore, to compare tumor detection by micro-computed tomography (microCT) to magnetic resonance imaging (MRI) in individual mouse. Methods: SUV max values were calculated from [ 18 F]-DA and [ 18 F]-DOPA PET, tumor-to-liver ratios (TLR) were obtained and expression of NET, VMAT1 and VMAT2 was evaluated. Results: [ 18 F]-DA detected less metastatic lesions compared to [ 18 F]-DOPA. TLR values for liver metastases were 2.26–2.71 for [ 18 F]-DOPA and 1.83–2.83 for [ 18 F]-DA. A limited uptake of [ 18 F]-DA was found in s.c. tumors (TLR=0.22-0.27) compared to [ 18 F]-DOPA (TLR=1.56-2.24). Overall, NET and VMAT2 were expressed in all organ and s.c. tumors. However, s.c. tumors lacked expression of VMAT1. We confirmed [ 18 F]-DA's high affinity for the NET for its uptake and VMAT1 and VMAT2 for its storage and retention in pheochromocytoma cell vesicles. In contrast, [ 18 F]-DOPA was found to utilize only VMAT2. Conclusion: MRI was superior in the detection of all organ tumors compared to microCT and PET. [ 18 F]-DOPA had overall better sensitivity than [ 18 F]-DA for the detection of metastases. Subcutaneous tumors were localized only with [ 18 F]-DOPA, a finding that may reflect differences in expression of VMAT1 and VMAT2, perhaps similar to some patients with pheochromocytoma where [ 18 F]-DOPA provides better visualization of lesions than [ 18 F]-DA.

  12. Extending FDA guidance to include consumer medication information (CMI) delivery on mobile devices.

    Science.gov (United States)

    Sage, Adam; Blalock, Susan J; Carpenter, Delesha

    This paper describes the current state of consumer-focused mobile health application use and the current U.S. Food and Drug Administration (FDA) guidance on the distribution of consumer medication information (CMI), and discusses recommendations and considerations for the FDA to expand CMI guidance to include CMI in mobile applications. Smartphone-based health interventions have been linked to increased medication adherence and improved health outcomes. Trends in smartphone ownership present opportunities to more effectively communicate and disseminate medication information; however, current FDA guidance for CMI does not outline how to effectively communicate CMI on a mobile platform, particularly in regards to user-centered design and information sourcing. As evidence supporting the potential effectiveness of mobile communication in health care continues to increase, CMI developers, regulating entities, and researchers should take note. Although mobile-based CMI offers an innovative mechanism to deliver medication information, caution should be exercised. Specifically, considerations for developing mobile CMI include consumers' digital literacy, user experience (e.g., usability), and the quality and accuracy of new widely used sources of information (e.g., crowd-sourced reviews and ratings). Recommended changes to FDA guidance for CMI include altering the language about scientific accuracy to address more novel methods of information gathering (e.g., anecdotal experiences and Google Consumer Surveys) and including guidance for usability testing of mobile health applications. Copyright © 2016 Elsevier Inc. All rights reserved.

  13. FDA publishes conflict of interest rules for clinical trials. Food and Drug Administration.

    Science.gov (United States)

    James, J S

    1998-03-06

    The Food and Drug Administration (FDA) published new rules defining conflict of interests between drug companies and medical researchers and clinicians. Certain financial arrangements will need to be disclosed, although the FDA estimates that only one to ten percent of pharmaceutical companies will need to submit disclosures for one or more of their investigators. The purpose of the new rule is to prevent bias in safety and efficacy studies of drugs and medical devices. The full rule is published in the Federal Register.

  14. License - GenLibi | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...nse Update History of This Database Site Policy | Contact Us License - GenLibi | LSDB Archive ...

  15. License - ClEST | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...License Update History of This Database Site Policy | Contact Us License - ClEST | LSDB Archive ...

  16. Reverse screening methods to search for the protein targets of chemopreventive compounds

    Science.gov (United States)

    Huang, Hongbin; Zhang, Guigui; Zhou, Yuquan; Lin, Chenru; Chen, Suling; Lin, Yutong; Mai, Shangkang; Huang, Zunnan

    2018-05-01

    This article is a systematic review of reverse screening methods used to search for the protein targets of chemopreventive compounds or drugs. Typical chemopreventive compounds include components of traditional Chinese medicine, natural compounds and Food and Drug Administration (FDA)-approved drugs. Such compounds are somewhat selective but are predisposed to bind multiple protein targets distributed throughout diverse signaling pathways in human cells. In contrast to conventional virtual screening, which identifies the ligands of a targeted protein from a compound database, reverse screening is used to identify the potential targets or unintended targets of a given compound from a large number of receptors by examining their known ligands or crystal structures. This method, also known as in silico or computational target fishing, is highly valuable for discovering the target receptors of query molecules from terrestrial or marine natural products, exploring the molecular mechanisms of chemopreventive compounds, finding alternative indications of existing drugs by drug repositioning, and detecting adverse drug reactions and drug toxicity. Reverse screening can be divided into three major groups: shape screening, pharmacophore screening and reverse docking. Several large software packages, such as Schrödinger and Discovery Studio; typical software/network services such as ChemMapper, PharmMapper, idTarget and INVDOCK; and practical databases of known target ligands and receptor crystal structures, such as ChEMBL, BindingDB and the Protein Data Bank (PDB), are available for use in these computational methods. Different programs, online services and databases have different applications and constraints. Here, we conducted a systematic analysis and multilevel classification of the computational programs, online services and compound libraries available for shape screening, pharmacophore screening and reverse docking to enable non-specialist users to quickly learn and

  17. INIS: Manual for online retrieval from the INIS Database on the Internet

    International Nuclear Information System (INIS)

    2000-01-01

    This manual demonstrates the different Search Forms available to retrieve relevant records using the INIS Database online retrieval system. Information on how to search, how to store, refine and retrieve searches, and how to update a literature search is given

  18. INIS: Manual for online retrieval from the INIS Database on the Internet

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2000-10-01

    This manual demonstrates the different Search Forms available to retrieve relevant records using the INIS Database online retrieval system. Information on how to search, how to store, refine and retrieve searches, and how to update a literature search is given.

  19. Download - fRNAdb | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...Download License Update History of This Database Site Policy | Contact Us Download - fRNAdb | LSDB Archive ...

  20. Download - TogoTV | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ... Download License Update History of This Database Site Policy | Contact Us Download - TogoTV | LSDB Archive ...

  1. A new relational database structure and online interface for the HITRAN database

    Science.gov (United States)

    Hill, Christian; Gordon, Iouli E.; Rothman, Laurence S.; Tennyson, Jonathan

    2013-11-01

    A new format for the HITRAN database is proposed. By storing the line-transition data in a number of linked tables described by a relational database schema, it is possible to overcome the limitations of the existing format, which have become increasingly apparent over the last few years as new and more varied data are being used by radiative-transfer models. Although the database in the new format can be searched using the well-established Structured Query Language (SQL), a web service, HITRANonline, has been deployed to allow users to make most common queries of the database using a graphical user interface in a web page. The advantages of the relational form of the database to ensuring data integrity and consistency are explored, and the compatibility of the online interface with the emerging standards of the Virtual Atomic and Molecular Data Centre (VAMDC) project is discussed. In particular, the ability to access HITRAN data using a standard query language from other websites, command line tools and from within computer programs is described.

  2. Hmrbase: a database of hormones and their receptors

    Science.gov (United States)

    Rashid, Mamoon; Singla, Deepak; Sharma, Arun; Kumar, Manish; Raghava, Gajendra PS

    2009-01-01

    Background Hormones are signaling molecules that play vital roles in various life processes, like growth and differentiation, physiology, and reproduction. These molecules are mostly secreted by endocrine glands, and transported to target organs through the bloodstream. Deficient, or excessive, levels of hormones are associated with several diseases such as cancer, osteoporosis, diabetes etc. Thus, it is important to collect and compile information about hormones and their receptors. Description This manuscript describes a database called Hmrbase which has been developed for managing information about hormones and their receptors. It is a highly curated database for which information has been collected from the literature and the public databases. The current version of Hmrbase contains comprehensive information about ~2000 hormones, e.g., about their function, source organism, receptors, mature sequences, structures etc. Hmrbase also contains information about ~3000 hormone receptors, in terms of amino acid sequences, subcellular localizations, ligands, and post-translational modifications etc. One of the major features of this database is that it provides data about ~4100 hormone-receptor pairs. A number of online tools have been integrated into the database, to provide the facilities like keyword search, structure-based search, mapping of a given peptide(s) on the hormone/receptor sequence, sequence similarity search. This database also provides a number of external links to other resources/databases in order to help in the retrieving of further related information. Conclusion Owing to the high impact of endocrine research in the biomedical sciences, the Hmrbase could become a leading data portal for researchers. The salient features of Hmrbase are hormone-receptor pair-related information, mapping of peptide stretches on the protein sequences of hormones and receptors, Pfam domain annotations, categorical browsing options, online data submission, Drug

  3. Biological Mesh Implants for Abdominal Hernia Repair: US Food and Drug Administration Approval Process and Systematic Review of Its Efficacy.

    Science.gov (United States)

    Huerta, Sergio; Varshney, Anubodh; Patel, Prachi M; Mayo, Helen G; Livingston, Edward H

    2016-04-01

    Expensive biological mesh materials are increasingly used to reinforce abdominal wall hernia repairs. The clinical and cost benefit of these materials are unknown. To review the published evidence on the use of biological mesh materials and to examine the US Food and Drug Administration (FDA) approval history for these devices. Search of multiple electronic databases (Ovid, MEDLINE, EMBASE, Cochrane Systematic Reviews, Cochrane Database of Abstracts of Reviews of Effects, Cochrane Central Register of Controlled Trials, and Cochrane National Health Service Economic Evaluation Database) to identify articles published between 1948 and June 30, 2015, on the use of biological mesh materials used to reinforce abdominal wall hernia repair. Keywords searched included surgical mesh, abdominal hernia, recurrence, infection, fistula, bioprosthesis, biocompatible materials, absorbable implants, dermis, and collagen. The FDA online database for 510(k) clearances was reviewed for all commercially available biological mesh materials. The median national price for mesh materials was established by a benchmarking query through several Integrated Delivery Network and Group Purchasing Organization tools. Of 274 screened articles, 20 met the search criteria. Most were case series that reported results of convenience samples of patients at single institutions with a variety of clinical problems. Only 3 of the 20 were comparative studies. There were no randomized clinical trials. In total, outcomes for 1033 patients were described. Studies varied widely in follow-up time, operative technique, meshes used, and patient selection criteria. Reported outcomes and clinical outcomes, such as fistula formation and infection, were inconsistently reported across studies. Conflicts of interest were not reported in 16 of the 20 studies. Recurrence rates ranged from 0% to 80%. All biological mesh devices were approved by the FDA based on substantial equivalence to a group of nonbiological predicate

  4. Evidential significance of automotive paint trace evidence using a pattern recognition based infrared library search engine for the Paint Data Query Forensic Database.

    Science.gov (United States)

    Lavine, Barry K; White, Collin G; Allen, Matthew D; Fasasi, Ayuba; Weakley, Andrew

    2016-10-01

    A prototype library search engine has been further developed to search the infrared spectral libraries of the paint data query database to identify the line and model of a vehicle from the clear coat, surfacer-primer, and e-coat layers of an intact paint chip. For this study, search prefilters were developed from 1181 automotive paint systems spanning 3 manufacturers: General Motors, Chrysler, and Ford. The best match between each unknown and the spectra in the hit list generated by the search prefilters was identified using a cross-correlation library search algorithm that performed both a forward and backward search. In the forward search, spectra were divided into intervals and further subdivided into windows (which corresponds to the time lag for the comparison) within those intervals. The top five hits identified in each search window were compiled; a histogram was computed that summarized the frequency of occurrence for each library sample, with the IR spectra most similar to the unknown flagged. The backward search computed the frequency and occurrence of each line and model without regard to the identity of the individual spectra. Only those lines and models with a frequency of occurrence greater than or equal to 20% were included in the final hit list. If there was agreement between the forward and backward search results, the specific line and model common to both hit lists was always the correct assignment. Samples assigned to the same line and model by both searches are always well represented in the library and correlate well on an individual basis to specific library samples. For these samples, one can have confidence in the accuracy of the match. This was not the case for the results obtained using commercial library search algorithms, as the hit quality index scores for the top twenty hits were always greater than 99%. Copyright © 2016 Elsevier B.V. All rights reserved.

  5. A new relational database structure and online interface for the HITRAN database

    International Nuclear Information System (INIS)

    Hill, Christian; Gordon, Iouli E.; Rothman, Laurence S.; Tennyson, Jonathan

    2013-01-01

    A new format for the HITRAN database is proposed. By storing the line-transition data in a number of linked tables described by a relational database schema, it is possible to overcome the limitations of the existing format, which have become increasingly apparent over the last few years as new and more varied data are being used by radiative-transfer models. Although the database in the new format can be searched using the well-established Structured Query Language (SQL), a web service, HITRANonline, has been deployed to allow users to make most common queries of the database using a graphical user interface in a web page. The advantages of the relational form of the database to ensuring data integrity and consistency are explored, and the compatibility of the online interface with the emerging standards of the Virtual Atomic and Molecular Data Centre (VAMDC) project is discussed. In particular, the ability to access HITRAN data using a standard query language from other websites, command line tools and from within computer programs is described. -- Highlights: • A new, interactive version of the HITRAN database is presented. • The data is stored in a structured fashion in a relational database. • The new HITRANonline interface offers increased functionality and easier error correction

  6. License - dbQSNP | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...escription Download License Update History of This Database Site Policy | Contact Us License - dbQSNP | LSDB Archive ...

  7. License - eSOL | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...iption Download License Update History of This Database Site Policy | Contact Us License - eSOL | LSDB Archive ...

  8. ExplorEnz: a MySQL database of the IUBMB enzyme nomenclature.

    Science.gov (United States)

    McDonald, Andrew G; Boyce, Sinéad; Moss, Gerard P; Dixon, Henry B F; Tipton, Keith F

    2007-07-27

    We describe the database ExplorEnz, which is the primary repository for EC numbers and enzyme data that are being curated on behalf of the IUBMB. The enzyme nomenclature is incorporated into many other resources, including the ExPASy-ENZYME, BRENDA and KEGG bioinformatics databases. The data, which are stored in a MySQL database, preserve the formatting of chemical and enzyme names. A simple, easy to use, web-based query interface is provided, along with an advanced search engine for more complex queries. The database is publicly available at http://www.enzyme-database.org. The data are available for download as SQL and XML files via FTP. ExplorEnz has powerful and flexible search capabilities and provides the scientific community with the most up-to-date version of the IUBMB Enzyme List.

  9. Fisher, Neyman, and Bayes at FDA.

    Science.gov (United States)

    Rubin, Donald B

    2016-01-01

    The wise use of statistical ideas in practice essentially requires some Bayesian thinking, in contrast to the classical rigid frequentist dogma. This dogma too often has seemed to influence the applications of statistics, even at agencies like the FDA. Greg Campbell was one of the most important advocates there for more nuanced modes of thought, especially Bayesian statistics. Because two brilliant statisticians, Ronald Fisher and Jerzy Neyman, are often credited with instilling the traditional frequentist approach in current practice, I argue that both men were actually seeking very Bayesian answers, and neither would have endorsed the rigid application of their ideas.

  10. Search of medical literature for indoor carbon monoxide exposure

    Energy Technology Data Exchange (ETDEWEB)

    Brennan, T.; Ivanovich, M.

    1995-12-01

    This report documents a literature search on carbon monoxide. The search was limited to the medical and toxicological databases at the National Library of Medicine (MEDLARS). The databases searched were Medline, Toxline and TOXNET. Searches were performed using a variety of strategies. Combinations of the following keywords were used: carbon, monoxide, accidental, residential, occult, diagnosis, misdiagnosis, heating, furnace, and indoor. The literature was searched from 1966 to the present. Over 1000 references were identified and summarized using the following abbreviations: The major findings of the search are: (1) Acute and subacute carbon monoxide exposures result in a large number of symptoms affecting the brain, kidneys, respiratory system, retina, and motor functions. (2) Acute and subacute carbon monoxide (CO) poisonings have been misdiagnosed on many occasions. (3) Very few systematic investigations have been made into the frequency and consequences of carbon monoxide poisonings.

  11. Issues in Big-Data Database Systems

    Science.gov (United States)

    2014-06-01

    that big data will not be manageable using conventional relational database technology, and it is true that alternative paradigms, such as NoSQL systems...conventional relational database technology, and it is true that alternative paradigms, such as NoSQL systems and search engines, have much to offer...scale well, and because integration with external data sources is so difficult. NoSQL systems are more open to this integration, and provide excellent

  12. VKCDB: Voltage-gated potassium channel database

    Directory of Open Access Journals (Sweden)

    Gallin Warren J

    2004-01-01

    Full Text Available Abstract Background The family of voltage-gated potassium channels comprises a functionally diverse group of membrane proteins. They help maintain and regulate the potassium ion-based component of the membrane potential and are thus central to many critical physiological processes. VKCDB (Voltage-gated potassium [K] Channel DataBase is a database of structural and functional data on these channels. It is designed as a resource for research on the molecular basis of voltage-gated potassium channel function. Description Voltage-gated potassium channel sequences were identified by using BLASTP to search GENBANK and SWISSPROT. Annotations for all voltage-gated potassium channels were selectively parsed and integrated into VKCDB. Electrophysiological and pharmacological data for the channels were collected from published journal articles. Transmembrane domain predictions by TMHMM and PHD are included for each VKCDB entry. Multiple sequence alignments of conserved domains of channels of the four Kv families and the KCNQ family are also included. Currently VKCDB contains 346 channel entries. It can be browsed and searched using a set of functionally relevant categories. Protein sequences can also be searched using a local BLAST engine. Conclusions VKCDB is a resource for comparative studies of voltage-gated potassium channels. The methods used to construct VKCDB are general; they can be used to create specialized databases for other protein families. VKCDB is accessible at http://vkcdb.biology.ualberta.ca.

  13. The ALADDIN atomic physics database system

    International Nuclear Information System (INIS)

    Hulse, R.A.

    1990-01-01

    ALADDIN is an atomic physics database system which has been developed in order to provide a broadly-based standard medium for the exchange and management of atomic data. ALADDIN consists of a data format definition together with supporting software for both interactive searches as well as for access to the data by plasma modeling and other codes. 8AB The ALADDIN system is designed to offer maximum flexibility in the choice of data representations and labeling schemes, so as to support a wide range of atomic physics data types and allow natural evolution and modification of the database as needs change. Associated dictionary files are included in the ALADDIN system for data documentation. The importance of supporting the widest possible user community was also central to be ALADDIN design, leading to the use of straightforward text files with concatentated data entries for the file structure, and the adoption of strict FORTRAN 77 code for the supporting software. This will allow ready access to the ALADDIN system on the widest range of scientific computers, and easy interfacing with FORTRAN modeling codes, user developed atomic physics codes and database, etc. This supporting software consists of the ALADDIN interactive searching and data display code, together with the ALPACK subroutine package which provides ALADDIN datafile searching and data retrieval capabilities to user's codes

  14. Three Drugs Approved for Urothelial Carcinoma by FDA.

    Science.gov (United States)

    2017-07-01

    The FDA has approved one PD-1 checkpoint inhibitor, pembrolizumab, and two PD-L1 checkpoint inhibitors, avelumab and durvalumab, to treat metastatic urothelial carcinoma in patients whose disease continues to progress despite platinum-based chemotherapy. This brings the total number of checkpoint inhibitors for the disease to five, prompting questions about how best to use them. ©2017 American Association for Cancer Research.

  15. Construction of Database for Pulsating Variable Stars

    Science.gov (United States)

    Chen, B. Q.; Yang, M.; Jiang, B. W.

    2011-07-01

    A database for the pulsating variable stars is constructed for Chinese astronomers to study the variable stars conveniently. The database includes about 230000 variable stars in the Galactic bulge, LMC and SMC observed by the MACHO (MAssive Compact Halo Objects) and OGLE (Optical Gravitational Lensing Experiment) projects at present. The software used for the construction is LAMP, i.e., Linux+Apache+MySQL+PHP. A web page is provided to search the photometric data and the light curve in the database through the right ascension and declination of the object. More data will be incorporated into the database.

  16. DEPOT database: Reference manual and user's guide

    International Nuclear Information System (INIS)

    Clancey, P.; Logg, C.

    1991-03-01

    DEPOT has been developed to provide tracking for the Stanford Linear Collider (SLC) control system equipment. For each piece of equipment entered into the database, complete location, service, maintenance, modification, certification, and radiation exposure histories can be maintained. To facilitate data entry accuracy, efficiency, and consistency, barcoding technology has been used extensively. DEPOT has been an important tool in improving the reliability of the microsystems controlling SLC. This document describes the components of the DEPOT database, the elements in the database records, and the use of the supporting programs for entering data, searching the database, and producing reports from the information

  17. Testing search strategies for systematic reviews in the Medline literature database through PubMed.

    Science.gov (United States)

    Volpato, Enilze S N; Betini, Marluci; El Dib, Regina

    2014-04-01

    A high-quality electronic search is essential in ensuring accuracy and completeness in retrieved records for the conducting of a systematic review. We analysed the available sample of search strategies to identify the best method for searching in Medline through PubMed, considering the use or not of parenthesis, double quotation marks, truncation and use of a simple search or search history. In our cross-sectional study of search strategies, we selected and analysed the available searches performed during evidence-based medicine classes and in systematic reviews conducted in the Botucatu Medical School, UNESP, Brazil. We analysed 120 search strategies. With regard to the use of phrase searches with parenthesis, there was no difference between the results with and without parenthesis and simple searches or search history tools in 100% of the sample analysed (P = 1.0). The number of results retrieved by the searches analysed was smaller using double quotations marks and using truncation compared with the standard strategy (P = 0.04 and P = 0.08, respectively). There is no need to use phrase-searching parenthesis to retrieve studies; however, we recommend the use of double quotation marks when an investigator attempts to retrieve articles in which a term appears to be exactly the same as what was proposed in the search form. Furthermore, we do not recommend the use of truncation in search strategies in the Medline via PubMed. Although the results of simple searches or search history tools were the same, we recommend using the latter.

  18. Clone - ClEST | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...le URL: ftp://ftp.biosciencedbc.jp/archive/clest/LATEST/clest_clone.zip File size: 660 KB Simple search URL ...ion Download License Update History of This Database Site Policy | Contact Us Clone - ClEST | LSDB Archive ...

  19. Image files - RPD | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...ftp://ftp.biosciencedbc.jp/archive/rpd/LATEST/rpd_gel_image.zip File size: 38.5 MB Simple search URL - Data ... License Update History of This Database Site Policy | Contact Us Image files - RPD | LSDB Archive ...

  20. A common feature pharmacophore for FDA-approved drugs inhibiting the Ebola virus [v2; ref status: indexed, http://f1000r.es/4wt

    Directory of Open Access Journals (Sweden)

    Sean Ekins

    2014-12-01

    Full Text Available We are currently faced with a global infectious disease crisis which has been anticipated for decades. While many promising biotherapeutics are being tested, the search for a small molecule has yet to deliver an approved drug or therapeutic for the Ebola or similar filoviruses that cause haemorrhagic fever. Two recent high throughput screens published in 2013 did however identify several hits that progressed to animal studies that are FDA approved drugs used for other indications. The current computational analysis uses these molecules from two different structural classes to construct a common features pharmacophore. This ligand-based pharmacophore implicates a possible common target or mechanism that could be further explored. A recent structure based design project yielded nine co-crystal structures of pyrrolidinone inhibitors bound to the viral protein 35 (VP35. When receptor-ligand pharmacophores based on the analogs of these molecules and the protein structures were constructed, the molecular features partially overlapped with the common features of solely ligand-based pharmacophore models based on FDA approved drugs. These previously identified FDA approved drugs with activity against Ebola were therefore docked into this protein. The antimalarials chloroquine and amodiaquine docked favorably in VP35. We propose that these drugs identified to date as inhibitors of the Ebola virus may be targeting VP35. These computational models may provide preliminary insights into the molecular features that are responsible for their activity against Ebola virus in vitro and in vivo and we propose that this hypothesis could be readily tested.

  1. A common feature pharmacophore for FDA-approved drugs inhibiting the Ebola virus [v1; ref status: indexed, http://f1000r.es/4qh

    Directory of Open Access Journals (Sweden)

    Sean Ekins

    2014-11-01

    Full Text Available We are currently faced with a global infectious disease crisis which has been anticipated for decades. While many promising biotherapeutics are being tested, the search for a small molecule has yet to deliver an approved drug or therapeutic for the Ebola or similar filoviruses that cause haemorrhagic fever. Two recent high throughput screens published in 2013 did however identify several hits that progressed to animal studies that are FDA approved drugs used for other indications. The current computational analysis uses these molecules from two different structural classes to construct a common features pharmacophore. This ligand-based pharmacophore implicates a possible common target or mechanism that could be further explored. A recent structure based design project yielded nine co-crystal structures of pyrrolidinone inhibitors bound to the viral protein 35 (VP35. When receptor-ligand pharmacophores based on the analogs of these molecules and the protein structures were constructed, the molecular features partially overlapped with the common features of solely ligand-based pharmacophore models based on FDA approved drugs. These previously identified FDA approved drugs with activity against Ebola were therefore docked into this protein. The antimalarials chloroquine and amodiaquine docked favorably in VP35. We propose that these drugs identified to date as inhibitors of the Ebola virus may be targeting VP35. These computational models may provide preliminary insights into the molecular features that are responsible for their activity against Ebola virus in vitro and in vivo and we propose that this hypothesis could be readily tested.

  2. [The practice of systematic reviews. II. Searching and selection of studies

    DEFF Research Database (Denmark)

    Assendelft, W J; van Tulder, M W; Scholten, R J

    1999-01-01

    can be performed in trial registers and printed indexes and by correspondence with experts and hand searching of journals. Storage of the search results in a bibliographic database is recommended. Various methodological problems may play a role in searching and selecting studies for a review: studies......Structured searching and selection of studies is an important component of a systematic review. It is recommended to record the various steps in a protocol in advance. The thoroughness of the searching and selection will partially depend on the available resources, like manpower and funds. A search...... action should be based on an unequivocally formulated research or clinical question, that is operationalized into clear inclusion and exclusion criteria. The actual start of a search strategy is a search in preferably multiple databases like Medline and EMBASE-Excerpta Medica. Additional search actions...

  3. A framework for intelligent data acquisition and real-time database searching for shotgun proteomics.

    Science.gov (United States)

    Graumann, Johannes; Scheltema, Richard A; Zhang, Yong; Cox, Jürgen; Mann, Matthias

    2012-03-01

    In the analysis of complex peptide mixtures by MS-based proteomics, many more peptides elute at any given time than can be identified and quantified by the mass spectrometer. This makes it desirable to optimally allocate peptide sequencing and narrow mass range quantification events. In computer science, intelligent agents are frequently used to make autonomous decisions in complex environments. Here we develop and describe a framework for intelligent data acquisition and real-time database searching and showcase selected examples. The intelligent agent is implemented in the MaxQuant computational proteomics environment, termed MaxQuant Real-Time. It analyzes data as it is acquired on the mass spectrometer, constructs isotope patterns and SILAC pair information as well as controls MS and tandem MS events based on real-time and prior MS data or external knowledge. Re-implementing a top10 method in the intelligent agent yields similar performance to the data dependent methods running on the mass spectrometer itself. We demonstrate the capabilities of MaxQuant Real-Time by creating a real-time search engine capable of identifying peptides "on-the-fly" within 30 ms, well within the time constraints of a shotgun fragmentation "topN" method. The agent can focus sequencing events onto peptides of specific interest, such as those originating from a specific gene ontology (GO) term, or peptides that are likely modified versions of already identified peptides. Finally, we demonstrate enhanced quantification of SILAC pairs whose ratios were poorly defined in survey spectra. MaxQuant Real-Time is flexible and can be applied to a large number of scenarios that would benefit from intelligent, directed data acquisition. Our framework should be especially useful for new instrument types, such as the quadrupole-Orbitrap, that are currently becoming available.

  4. Classical databases and knowledge organization

    DEFF Research Database (Denmark)

    Hjørland, Birger

    2015-01-01

    This paper considers classical bibliographic databases based on the Boolean retrieval model (such as MEDLINE and PsycInfo). This model is challenged by modern search engines and information retrieval (IR) researchers, who often consider Boolean retrieval a less efficient approach. The paper...

  5. Guide to QSPIRES and the particle physics databases on SLACVM

    International Nuclear Information System (INIS)

    Galic, H.

    1992-06-01

    SLAC, in collarboration with DESY, LBL, and several other institutions, maintains many databases of interest to the high energy physics community. You do not to have a computer account at SLAC to search through some of these databases, they can be reached via the remote server QSPIRES, set at the BITNET node SLACVM. This text describes, in great detail, how to search in the popular HEP database via QSPIRES, HEP contains bibliographic summaries of more than 200,000 particle physics papers. Other databases available remotely are also reviewed, and the registration procedure for those who would like to use QSPIRES is explained. To utilize QSPIRES, you must have access to a large computer network. It is not necessary that the network be BITNET; it may be a different one. However, a gateway must exist between your network and BITNET. It should be mentioned at BITNET users have some advantages in searching, e.g., the possibility of interactive communication with QSPIRES. Therefore, if you have a choice, let a BITNET machine be your base for QSPIRES searches. You will also need an authorization to use HEP and other databases; and should know the set of relevant commands and rules. The authorization is free, the commands are simple, and BITNET can be reached from all over the world. Join, therefore, the group of thousands of satisfied users, log on to your local computer, and from the comfort of your office or home fine, e.g., the number of citations of your most famous high energy physics paper

  6. Guide to QSPIRES and the particle physics databases on SLACVM

    Energy Technology Data Exchange (ETDEWEB)

    Galic, H.

    1992-06-01

    SLAC, in collarboration with DESY, LBL, and several other institutions, maintains many databases of interest to the high energy physics community. You do not to have a computer account at SLAC to search through some of these databases, they can be reached via the remote server QSPIRES, set at the BITNET node SLACVM. This text describes, in great detail, how to search in the popular HEP database via QSPIRES, HEP contains bibliographic summaries of more than 200,000 particle physics papers. Other databases available remotely are also reviewed, and the registration procedure for those who would like to use QSPIRES is explained. To utilize QSPIRES, you must have access to a large computer network. It is not necessary that the network be BITNET; it may be a different one. However, a gateway must exist between your network and BITNET. It should be mentioned at BITNET users have some advantages in searching, e.g., the possibility of interactive communication with QSPIRES. Therefore, if you have a choice, let a BITNET machine be your base for QSPIRES searches. You will also need an authorization to use HEP and other databases; and should know the set of relevant commands and rules. The authorization is free, the commands are simple, and BITNET can be reached from all over the world. Join, therefore, the group of thousands of satisfied users, log on to your local computer, and from the comfort of your office or home fine, e.g., the number of citations of your most famous high energy physics paper.

  7. Right to experimental treatment: FDA new drug approval, constitutional rights, and the public's health.

    Science.gov (United States)

    Leonard, Elizabeth Weeks

    2009-01-01

    On May 2, 2006, a divided panel of the U.S. Court of Appeals for the District of Columbia, in a startling opinion, Abigail Alliance for Better Access to Developmental Drugs v. Eschenbach, held that terminally ill patients who have exhausted all other available options have a constitutional right to experimental treatment that FDA has not yet approved. Although ultimately overturned by the full court, Abigail Alliance generated considerable interest from various constituencies. Meanwhile, FDA proposed similar regulatory amendments, as have lawmakers on both sides of the aisle in Congress. But proponents of expanded access fail to consider public health and consumer safety concerns. In particular, allowing patients to try unproven treatments, outside of controlled clinical trials risks both the study's outcome and the health of patients who might benefit from the deliberate, careful process of new drug approval as it currently operates under FDA's auspices.

  8. The reactive metabolite target protein database (TPDB)--a web-accessible resource.

    Science.gov (United States)

    Hanzlik, Robert P; Koen, Yakov M; Theertham, Bhargav; Dong, Yinghua; Fang, Jianwen

    2007-03-16

    The toxic effects of many simple organic compounds stem from their biotransformation to chemically reactive metabolites which bind covalently to cellular proteins. To understand the mechanisms of cytotoxic responses it may be important to know which proteins become adducted and whether some may be common targets of multiple toxins. The literature of this field is widely scattered but expanding rapidly, suggesting the need for a comprehensive, searchable database of reactive metabolite target proteins. The Reactive Metabolite Target Protein Database (TPDB) is a comprehensive, curated, searchable, documented compilation of publicly available information on the protein targets of reactive metabolites of 18 well-studied chemicals and drugs of known toxicity. TPDB software enables i) string searches for author names and proteins names/synonyms, ii) more complex searches by selecting chemical compound, animal species, target tissue and protein names/synonyms from pull-down menus, and iii) commonality searches over multiple chemicals. Tabulated search results provide information, references and links to other databases. The TPDB is a unique on-line compilation of information on the covalent modification of cellular proteins by reactive metabolites of chemicals and drugs. Its comprehensiveness and searchability should facilitate the elucidation of mechanisms of reactive metabolite toxicity. The database is freely available at http://tpdb.medchem.ku.edu/tpdb.html.

  9. Geologic Field Database

    Directory of Open Access Journals (Sweden)

    Katarina Hribernik

    2002-12-01

    Full Text Available The purpose of the paper is to present the field data relational database, which was compiled from data, gathered during thirty years of fieldwork on the Basic Geologic Map of Slovenia in scale1:100.000. The database was created using MS Access software. The MS Access environment ensures its stability and effective operation despite changing, searching, and updating the data. It also enables faster and easier user-friendly access to the field data. Last but not least, in the long-term, with the data transferred into the GISenvironment, it will provide the basis for the sound geologic information system that will satisfy a broad spectrum of geologists’ needs.

  10. Nuclear data processing using a database management system

    International Nuclear Information System (INIS)

    Castilla, V.; Gonzalez, L.

    1991-01-01

    A database management system that permits the design of relational models was used to create an integrated database with experimental and evaluated nuclear data.A system that reduces the time and cost of processing was created for computers type EC or compatibles.A set of programs for the conversion from nuclear calculated data output format to EXFOR format was developed.A dictionary to perform a retrospective search in the ENDF database was created too

  11. tRNA - RMG | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...File URL: ftp://ftp.biosciencedbc.jp/archive/rmg/LATEST/rmg_trna.zip File size: 1 KB Simple search URL http:...ption Download License Update History of This Database Site Policy | Contact Us tRNA - RMG | LSDB Archive ...

  12. Interactive Multi-Instrument Database of Solar Flares

    Science.gov (United States)

    Ranjan, Shubha S.; Spaulding, Ryan; Deardorff, Donald G.

    2018-01-01

    The fundamental motivation of the project is that the scientific output of solar research can be greatly enhanced by better exploitation of the existing solar/heliosphere space-data products jointly with ground-based observations. Our primary focus is on developing a specific innovative methodology based on recent advances in "big data" intelligent databases applied to the growing amount of high-spatial and multi-wavelength resolution, high-cadence data from NASA's missions and supporting ground-based observatories. Our flare database is not simply a manually searchable time-based catalog of events or list of web links pointing to data. It is a preprocessed metadata repository enabling fast search and automatic identification of all recorded flares sharing a specifiable set of characteristics, features, and parameters. The result is a new and unique database of solar flares and data search and classification tools for the Heliophysics community, enabling multi-instrument/multi-wavelength investigations of flare physics and supporting further development of flare-prediction methodologies.

  13. Novel LOVD databases for hereditary breast cancer and colorectal cancer genes in the Chinese population.

    Science.gov (United States)

    Pan, Min; Cong, Peikuan; Wang, Yue; Lin, Changsong; Yuan, Ying; Dong, Jian; Banerjee, Santasree; Zhang, Tao; Chen, Yanling; Zhang, Ting; Chen, Mingqing; Hu, Peter; Zheng, Shu; Zhang, Jin; Qi, Ming

    2011-12-01

    The Human Variome Project (HVP) is an international consortium of clinicians, geneticists, and researchers from over 30 countries, aiming to facilitate the establishment and maintenance of standards, systems, and infrastructure for the worldwide collection and sharing of all genetic variations effecting human disease. The HVP-China Node will build new and supplement existing databases of genetic diseases. As the first effort, we have created a novel variant database of BRCA1 and BRCA2, mismatch repair genes (MMR), and APC genes for breast cancer, Lynch syndrome, and familial adenomatous polyposis (FAP), respectively, in the Chinese population using the Leiden Open Variation Database (LOVD) format. We searched PubMed and some Chinese search engines to collect all the variants of these genes in the Chinese population that have already been detected and reported. There are some differences in the gene variants between the Chinese population and that of other ethnicities. The database is available online at http://www.genomed.org/LOVD/. Our database will appear to users who survey other LOVD databases (e.g., by Google search, or by NCBI GeneTests search). Remote submissions are accepted, and the information is updated monthly. © 2011 Wiley Periodicals, Inc.

  14. FDA: polyurethane condom carries "extremely misleading" label. Federal agency allows distribution for public health's sake.

    Science.gov (United States)

    1995-02-01

    The labeling of the Avanti polyurethane condom selling in 10 Western states makes misleading claims about protection from pregnancy and sexually transmitted diseases (STDs) according to officials at the US Food and Drug Administration (FDA). Avanti is sold in a foil package printed with the claim that it is effective against pregnancy, HIV, and STDs. However, polyurethane condoms have not undergone clinical efficacy testing for contraception or STDs, according to officials. The manufacturer of the condom refuted this allegation, stating that latex condoms have the same claims on them. In early 1995 the FDA met with the manufacturer and other companies developing plastic condoms, and concluded that these condoms could not make such claims, nor any claims about slippage and breakage rates. Despite warnings in 1993 to the manufacturer of Avanti about labeling restrictions, the company printed pregnancy and STD efficacy claims on the boxes and individual packages. The FDA later worked out a compromise with the firm in which only the boxes had to be reprinted with the generic label. The FDA had to weigh the risk of the public health cost of delaying sale of the condom, which is the first impermeable condom proven safe for people with latex allergies. In 1991 the FDA was defining standards for clinical testing and labeling of polyurethane condoms under congressional mandate, but the manufacturer of Avanti began mass production based on a preliminary approval determining that the condom was equivalent to latex condoms already on the market. 7000 Avanti condoms were subsequently tested in five countries, but these user tests did not compare Avanti to latex condoms and did not test for pregnancy and STD protection. Test results submitted to the FDA by the company indicated that, although Avanti is more than 1/3 less elastic than latex condoms, it did not break more frequently in an in-use study involving 187 couples.

  15. NUCDAS: a database of nuclear criticality data around the world

    International Nuclear Information System (INIS)

    Komuro, Yuichi; Sakai, Tomohiro

    1999-01-01

    The NUCDAS database, which contains great numbers of nuclear criticality data and subcritical limit data described in criticality safety handbooks of Japan and foreign countries, has been developed at JAERI. The database was designed to perform quick search on criticality data and subcritical limits and to draw their curves for comparison. So, criticality data among handbooks can be shown on the screen and/or printed on the paper. The database runs on the Apple Macintosh computer and written in 4th Dimension, a relational database software for the Macintosh. This tool provides powerful search and sort capabilities. An appropriate graphic software (e.g. KaleidaGraph) is used to draw a graph of selected criticality data. NUCDAS will be demonstrated in the poster presentation. NUCEF'98 participants who are interested in NUCDAS will be able to operate Macintosh with the database and will be encouraged to give us some comments on it for modifications. Though all messages on the screen are written in Japanese, don't worry. (author)

  16. Comparison of treatment effect sizes from pivotal and postapproval trials of novel therapeutics approved by the FDA based on surrogate markers of disease: a meta-epidemiological study.

    Science.gov (United States)

    Wallach, Joshua D; Ciani, Oriana; Pease, Alison M; Gonsalves, Gregg S; Krumholz, Harlan M; Taylor, Rod S; Ross, Joseph S

    2018-03-21

    The U.S. Food and Drug Administration (FDA) often approves new drugs based on trials that use surrogate markers for endpoints, which involve certain trade-offs and may risk making erroneous inferences about the medical product's actual clinical effect. This study aims to compare the treatment effects among pivotal trials supporting FDA approval of novel therapeutics based on surrogate markers of disease with those observed among postapproval trials for the same indication. We searched Drugs@FDA and PubMed to identify published randomized superiority design pivotal trials for all novel drugs initially approved by the FDA between 2005 and 2012 based on surrogate markers as primary endpoints and published postapproval trials using the same surrogate markers or patient-relevant outcomes as endpoints. Summary ratio of odds ratios (RORs) and difference between standardized mean differences (dSMDs) were used to quantify the average difference in treatment effects between pivotal and matched postapproval trials. Between 2005 and 2012, the FDA approved 88 novel drugs for 90 indications based on one or multiple pivotal trials using surrogate markers of disease. Of these, 27 novel drugs for 27 indications were approved based on pivotal trials using surrogate markers as primary endpoints that could be matched to at least one postapproval trial, for a total of 43 matches. For nine (75.0%) of the 12 matches using the same non-continuous surrogate markers as trial endpoints, pivotal trials had larger treatment effects than postapproval trials. On average, treatment effects were 50% higher (more beneficial) in the pivotal than the postapproval trials (ROR 1.5; 95% confidence interval CI 1.01-2.23). For 17 (54.8%) of the 31 matches using the same continuous surrogate markers as trial endpoints, pivotal trials had larger treatment effects than the postapproval trials. On average, there was no difference in treatment effects between pivotal and postapproval trials (dSMDs 0.01; 95

  17. TOPDOM: database of conservatively located domains and motifs in proteins.

    Science.gov (United States)

    Varga, Julia; Dobson, László; Tusnády, Gábor E

    2016-09-01

    The TOPDOM database-originally created as a collection of domains and motifs located consistently on the same side of the membranes in α-helical transmembrane proteins-has been updated and extended by taking into consideration consistently localized domains and motifs in globular proteins, too. By taking advantage of the recently developed CCTOP algorithm to determine the type of a protein and predict topology in case of transmembrane proteins, and by applying a thorough search for domains and motifs as well as utilizing the most up-to-date version of all source databases, we managed to reach a 6-fold increase in the size of the whole database and a 2-fold increase in the number of transmembrane proteins. TOPDOM database is available at http://topdom.enzim.hu The webpage utilizes the common Apache, PHP5 and MySQL software to provide the user interface for accessing and searching the database. The database itself is generated on a high performance computer. tusnady.gabor@ttk.mta.hu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  18. Quantum partial search for uneven distribution of multiple target items

    Science.gov (United States)

    Zhang, Kun; Korepin, Vladimir

    2018-06-01

    Quantum partial search algorithm is an approximate search. It aims to find a target block (which has the target items). It runs a little faster than full Grover search. In this paper, we consider quantum partial search algorithm for multiple target items unevenly distributed in a database (target blocks have different number of target items). The algorithm we describe can locate one of the target blocks. Efficiency of the algorithm is measured by number of queries to the oracle. We optimize the algorithm in order to improve efficiency. By perturbation method, we find that the algorithm runs the fastest when target items are evenly distributed in database.

  19. Effects of a random noisy oracle on search algorithm complexity

    International Nuclear Information System (INIS)

    Shenvi, Neil; Brown, Kenneth R.; Whaley, K. Birgitta

    2003-01-01

    Grover's algorithm provides a quadratic speed-up over classical algorithms for unstructured database or library searches. This paper examines the robustness of Grover's search algorithm to a random phase error in the oracle and analyzes the complexity of the search process as a function of the scaling of the oracle error with database or library size. Both the discrete- and continuous-time implementations of the search algorithm are investigated. It is shown that unless the oracle phase error scales as O(N -1/4 ), neither the discrete- nor the continuous-time implementation of Grover's algorithm is scalably robust to this error in the absence of error correction

  20. Database automation of accelerator operation

    International Nuclear Information System (INIS)

    Casstevens, B.J.; Ludemann, C.A.

    1983-01-01

    Database management techniques are applied to automating the setup of operating parameters of a heavy-ion accelerator used in nuclear physics experiments. Data files consist of ion-beam attributes, the interconnection assignments of the numerous power supplies and magnetic elements that steer the ions' path through the system, the data values that represent the electrical currents supplied by the power supplies, as well as the positions of motors and status of mechanical actuators. The database is relational and permits searching on ranges of any subset of the ion-beam attributes. A file selected from the database is used by the control software to replicate the ion beam conditions by adjusting the physical elements in a continuous manner